Bowtie 2 seems to be working fine (tested command '/home/shared/bowtie2-2.4.4-linux-x86_64/bowtie2 --version' [2.4.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/usr/bin/samtools' Reference genome folder provided is ../data/ (absolute path is '/home/shared/16TB_HDD_01/sr320/github/project-mytilus-methylation/data/)' FastQ format assumed (by default) Attention: using more than 4 cores per alignment thread has been reported to have diminishing returns. If possible try to limit -p to a value of 4 Each Bowtie 2 instance is going to be run with 8 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/home/shared/16TB_HDD_01/sr320/github/project-mytilus-methylation/code'): ../data/272M_R1.fastp-trim.fq.gz ../data/272M_R2.fastp-trim.fq.gz Library is assumed to be strand-specific (directional), alignments to strands complementary to the original top or bottom strands will be ignored (i.e. not performed!) Output will be written into the directory: /home/shared/16TB_HDD_01/sr320/github/project-mytilus-methylation/output/01.2-bismark/ Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-1.0 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /home/shared/16TB_HDD_01/sr320/github/project-mytilus-methylation/code Now reading in and storing sequence information of the genome specified in: /home/shared/16TB_HDD_01/sr320/github/project-mytilus-methylation/data/ Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are ../data/272M_R1.fastp-trim.fq.gz and ../data/272M_R2.fastp-trim.fq.gz Input files are in FastQ format Writing a C -> T converted version of the input file 272M_R1.fastp-trim.fq.gz to 272M_R1.fastp-trim.fq.gz_C_to_T.fastq Created C -> T converted version of the FastQ file 272M_R1.fastp-trim.fq.gz (89521685 sequences in total) Writing a G -> A converted version of the input file 272M_R2.fastp-trim.fq.gz to 272M_R2.fastp-trim.fq.gz_G_to_A.fastq Created G -> A converted version of the FastQ file 272M_R2.fastp-trim.fq.gz (89521685 sequences in total) Input files are 272M_R1.fastp-trim.fq.gz_C_to_T.fastq and 272M_R2.fastp-trim.fq.gz_G_to_A.fastq (FastQ) Now running 2 instances of Bowtie 2 against the bisulfite genome of /home/shared/16TB_HDD_01/sr320/github/project-mytilus-methylation/data/ with the specified options: -q --score-min L,0,-1.0 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from 272M_R1.fastp-trim.fq.gz_C_to_T.fastq and 272M_R2.fastp-trim.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.0 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: LH00469:254:22HGFVLT4:2:1101:2934:1014_1:N:0:GAAGTTGG+CGAACAAC/1 99 NC_086378.1_CT_converted 28632485 6 131M = 28632393 -223 GAATGTTTATTATGAGTAGTTGATTAAGTGTTGTAATTTTGGTGTAGATTTATTATTTAAGATGGTTTTTAGTGGGGGATTTAGTTAAATATAGGATTTTATGGGAAATGTATATAAATGATTTTTTTTAG IIIIIIIIIIIIIIIIIIIII99IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIII9IIII9III9I-IIIIIIIIIIIII99II9IIII9IIIII9IIIIIIIIIIIII AS:i:-36 XS:i:-54 XN:i:0 XM:i:6 XO:i:0 XG:i:0 NM:i:6 MD:Z:8T7G0T16T10T21G63 YS:i:-6 YT:Z:CP LH00469:254:22HGFVLT4:2:1101:2934:1014_2:N:0:GAAGTTGG+CGAACAAC/2 147 NC_086378.1_CT_converted 28632393 6 131M = 28632485 223 GGGGATTTAGTTAAATATAGGATTTTATGGGAAATGTATATAAATGATTTTTTTTAGAGAATTATTGAATGGAATGAAATTAAATATGGTATGAATGTTTATTATGAGGTGTTGATTAAGTGTTGTTATTT IIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIII-IIIIIIIIII9III9-IIIIIIIIIIIIIIII AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:100T30 YS:i:-36 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from 272M_R1.fastp-trim.fq.gz_C_to_T.fastq and 272M_R2.fastp-trim.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-1.0 -p 8 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: LH00469:254:22HGFVLT4:2:1101:2934:1014_1:N:0:GAAGTTGG+CGAACAAC/1 83 NC_086379.1_GA_converted 46183439 1 131M = 46183365 -205 CTAAAAAAAATCATTTATATACATTTCCCATAAAATCCTATATTTAACTAAATCCCCCACTAAAAACCATCTTAAATAATAAATCTACACCAAAATTACAACACTTAATCAACTACTCATAATAAACATTC IIIIIIIIIIIII9IIIII9IIII9II99IIIIIIIIIIIII-I9III9IIII9IIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIII99IIIIIIIIIIIIIIIIIIIII AS:i:-18 XS:i:-18 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:44A51A17C16 YS:i:-12 YT:Z:CP LH00469:254:22HGFVLT4:2:1101:2934:1014_2:N:0:GAAGTTGG+CGAACAAC/2 163 NC_086379.1_GA_converted 46183365 1 131M = 46183439 205 AAATAACAACACTTAATCAACACCTCATAATAAACATTCATACCATATTTAATTTCATTCCATTCAATAATTCTCTAAAAAAAATCATTTATATACATTTCCCATAAAATCCTATATTTAACTAAATCCCC IIIIIIIIIIIIIIII-9III9IIIIIIIIII-IIIIIIIIIIIIIIIIIIIIIII9IIIIIIIIIIII9IIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIIII9IIIIII AS:i:-12 XS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:59A58A12 YS:i:-18 YT:Z:CP >>> Writing bisulfite mapping results to 272M_pe.bam <<< Reading in the sequence files ../data/272M_R1.fastp-trim.fq.gz and ../data/272M_R2.fastp-trim.fq.gz Processed 1000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1119:26005:4082_1:N:0:GAAGTTGG+CGAACAAC NW_026963634.1 1 Processed 2000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1127:28999:5426_1:N:0:GAAGTTGG+CGAACAAC NC_086383.1 71253552 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1127:29007:5440_1:N:0:GAAGTTGG+CGAACAAC NC_086383.1 71253552 Processed 3000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1138:39600:25626_1:N:0:GAAGTTGG+CGAACAAC NW_026963402.1 95204 Processed 4000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1149:16780:20303_1:N:0:GAAGTTGG+CGAACAAC NW_026963415.1 2 Processed 5000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1159:20349:22950_1:N:0:GAAGTTGG+CGAACAAC NW_026963377.1 1 Processed 6000000 sequence pairs so far Processed 7000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1181:43856:4474_1:N:0:GAAGTTGG+CGAACAAC NW_026963307.1 124871 Processed 8000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1187:14037:8942_1:N:0:GAAGTTGG+CGAACAAC NW_026963307.1 124870 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1190:29816:16647_1:N:0:GAAGTTGG+CGAACAAC NW_026963461.1 39099 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1190:28141:20275_1:N:0:GAAGTTGG+CGAACAAC NC_086374.1 103707540 Processed 9000000 sequence pairs so far Processed 10000000 sequence pairs so far Processed 11000000 sequence pairs so far Processed 12000000 sequence pairs so far Processed 13000000 sequence pairs so far Processed 14000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1255:47174:6687_1:N:0:GAAGTTGG+CGAACAAC NW_026963598.1 2 Processed 15000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1266:24055:3535_1:N:0:GAAGTTGG+CGAACAAC NW_026963377.1 2 Processed 16000000 sequence pairs so far Processed 17000000 sequence pairs so far Processed 18000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1292:37892:8298_1:N:0:GAAGTTGG+CGAACAAC NW_026963804.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1292:37876:8326_1:N:0:GAAGTTGG+CGAACAAC NW_026963804.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1303:22291:4068_1:N:0:GAAGTTGG+CGAACAAC NW_026963744.1 22720 Processed 19000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1307:51512:11646_1:N:0:GAAGTTGG+CGAACAAC NW_026963375.1 53639 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1307:51528:11646_1:N:0:GAAGTTGG+CGAACAAC NW_026963375.1 53639 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1311:16845:10918_1:N:0:GAAGTTGG+CGAACAAC NW_026963424.1 91103 Processed 20000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1319:49723:3619_1:N:0:GAAGTCGG+CGAACAAC NW_026963315.1 4066329 Processed 21000000 sequence pairs so far Processed 22000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1341:13834:12122_1:N:0:GAAGTTGG+CGAACAAC NW_026963788.1 21674 Processed 23000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1344:44366:26004_1:N:0:GAAGTTGG+CGAACAAC NW_026963533.1 25116 Processed 24000000 sequence pairs so far Processed 25000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1374:38677:15848_1:N:0:GAAGTTGG+CGAACAAC NW_026963415.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1375:37172:6015_1:N:0:GAAGTTGG+CGAACAAC NW_026963415.1 2 Processed 26000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1380:43921:27279_1:N:0:GAAGTTGG+CGAACAAC NW_026963377.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1383:38451:3858_1:N:0:GAAGTTGG+CGAACAAC NW_026963772.1 2 Processed 27000000 sequence pairs so far Processed 28000000 sequence pairs so far Processed 29000000 sequence pairs so far Processed 30000000 sequence pairs so far Processed 31000000 sequence pairs so far Processed 32000000 sequence pairs so far Processed 33000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:1462:43363:11828_1:N:0:GAAGTTGG+CGAACAAC NW_026963293.1 499878 Processed 34000000 sequence pairs so far Processed 35000000 sequence pairs so far Processed 36000000 sequence pairs so far Processed 37000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2105:3444:14700_1:N:0:GAAGTTGG+CGAACAAC NW_026963377.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2105:3460:14700_1:N:0:GAAGTTGG+CGAACAAC NW_026963377.1 2 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2105:3452:14714_1:N:0:GAAGTTGG+CGAACAAC NW_026963377.1 2 Processed 38000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2117:1486:24393_1:N:0:GAAGTTGG+CGAACAAC NW_026963415.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2118:38928:1602_1:N:0:GAAGTTGG+CGAACAAC NW_026963443.1 2 Processed 39000000 sequence pairs so far Processed 40000000 sequence pairs so far Processed 41000000 sequence pairs so far Processed 42000000 sequence pairs so far Processed 43000000 sequence pairs so far Processed 44000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2184:14126:11282_1:N:0:GAAGTTGG+CGAACAAC NW_026963561.1 22617 Processed 45000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2192:30545:4432_1:N:0:GAAGTTGG+CGAACAAC NW_026963583.1 1 Processed 46000000 sequence pairs so far Processed 47000000 sequence pairs so far Processed 48000000 sequence pairs so far Processed 49000000 sequence pairs so far Processed 50000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2255:42562:22236_1:N:0:GAAGTTGG+CGAACAAC NW_026963299.1 2 Processed 51000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2266:20454:12486_1:N:0:GAAGTTGG+CGAACAAC NW_026963532.1 2 Processed 52000000 sequence pairs so far Processed 53000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2282:6996:10315_1:N:0:GAAGTTGG+CGAACAAC NW_026963789.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2291:6017:20163_1:N:0:GAAGTTGG+CGAACAAC NW_026963687.1 26553 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2291:18091:25037_1:N:0:GAAGTTGG+CGAACAAC NW_026963402.1 95213 Processed 54000000 sequence pairs so far Processed 55000000 sequence pairs so far Processed 56000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2328:12127:7093_1:N:0:GAAGTTGG+CGAACAAC NW_026963744.1 22710 Processed 57000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2334:18657:26494_1:N:0:GAAGTTGG+CGAACAAC NW_026963372.1 501124 Processed 58000000 sequence pairs so far Processed 59000000 sequence pairs so far Processed 60000000 sequence pairs so far Processed 61000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2378:17613:24659_1:N:0:GAAGTTGG+CGAACAAC NW_026963647.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2378:28773:26578_1:N:0:GAAGTTGG+CGAACAAC NW_026963717.1 2 Processed 62000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2397:9262:12192_1:N:0:GAAGTTGG+CGAACAAC NW_026963294.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2403:12879:12178_1:N:0:GAAGTTGG+CGAACAAC NW_026963293.1 499899 Processed 63000000 sequence pairs so far Processed 64000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2424:11034:15652_1:N:0:GAAGTTGG+CGAACAAC NW_026963744.1 22702 Processed 65000000 sequence pairs so far Processed 66000000 sequence pairs so far Processed 67000000 sequence pairs so far Processed 68000000 sequence pairs so far Processed 69000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2482:27866:12570_1:N:0:GAAGTTGG+CGAACAAC NW_026963415.1 1 Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2483:13794:27181_1:N:0:GAAGTTGG+CGAACAAC NW_026963582.1 2 Processed 70000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00469:254:22HGFVLT4:2:2492:4415:28231_1:N:0:GAAGTTGG+CGAACAAC NW_026963717.1 2 Processed 71000000 sequence pairs so far Processed 72000000 sequence pairs so far Processed 73000000 sequence pairs so far Processed 74000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1221:33150:13705_1:N:0:GAAGTTGG+CGAACAAC NW_026963322.1 898872 Processed 75000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1282:26814:21900_1:N:0:GAAGTTGG+CGAACAAC NW_026963415.1 2 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1302:31872:10679_1:N:0:GAAGTTGG+CGAACAAC NW_026963415.1 3 Processed 76000000 sequence pairs so far Processed 77000000 sequence pairs so far Processed 78000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1388:49011:2359_1:N:0:GAAGTTGG+CGAACAAC NW_026963443.1 1 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1416:28894:28805_1:N:0:GAAGTTGG+CGAACAAC NW_026963443.1 1 Processed 79000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:1435:32123:26718_1:N:0:GAAGTTGG+CGAACAAC NC_086376.1 1 Processed 80000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2110:17937:5581_1:N:0:GAAGTTGG+CGACCAAC NW_026963468.1 1 Processed 81000000 sequence pairs so far Processed 82000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2196:4884:28203_1:N:0:GAAGTTGG+CGAACAAC NW_026963711.1 22996 Processed 83000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2224:21522:1812_1:N:0:GAAGTTGG+CGAACAAC NW_026963634.1 1 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2241:47312:21241_1:N:0:GAAGTTGG+CGAACAAC NW_026963738.1 1 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2251:51026:27475_1:N:0:GAAGTTGG+CGAACAAC NW_026963443.1 56340 Processed 84000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2269:12499:9447_1:N:0:GAAGTTGG+CGAACAAC NW_026963684.1 18476 Processed 85000000 sequence pairs so far Processed 86000000 sequence pairs so far Processed 87000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2416:23351:1812_1:N:0:GAAGTTGG+CGAACAAC NW_026963315.1 4066329 Processed 88000000 sequence pairs so far Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2436:21376:6435_1:N:0:GAAGTTGG+CGAACAAC NW_026963362.1 1 Chromosomal sequence could not be extracted for LH00586:122:22HTFTLT4:7:2453:37998:20583_1:N:0:GAAGTTGG+CGAACAAC NW_026963704.1 21263 Processed 89000000 sequence pairs so far 89521685 reads; of these: 89521685 (100.00%) were paired; of these: 38845482 (43.39%) aligned concordantly 0 times 17514863 (19.56%) aligned concordantly exactly 1 time 33161340 (37.04%) aligned concordantly >1 times 56.61% overall alignment rate 89521685 reads; of these: 89521685 (100.00%) were paired; of these: 38860626 (43.41%) aligned concordantly 0 times 17494501 (19.54%) aligned concordantly exactly 1 time 33166558 (37.05%) aligned concordantly >1 times 56.59% overall alignment rate Processed 89521685 sequences in total Failed to close filehandle AMBIG_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2641, line 358086740. Failed to close filehandle AMBIG_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2642, line 358086740. Failed to close filehandle UNMAPPED_1: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2643, line 358086740. Failed to close filehandle UNMAPPED_2: Bad file descriptor at /home/shared/Bismark-0.24.0/bismark line 2644, line 358086740. Successfully deleted the temporary files 272M_R1.fastp-trim.fq.gz_C_to_T.fastq and 272M_R2.fastp-trim.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 89521685 Final Cytosine Methylation Report ================================= Total number of C's analysed: 2153931343 Total methylated C's in CpG context: 28572629 Total methylated C's in CHG context: 3301495 Total methylated C's in CHH context: 15504092 Total methylated C's in Unknown context: 399098 Total unmethylated C's in CpG context: 220109839 Total unmethylated C's in CHG context: 341255323 Total unmethylated C's in CHH context: 1545187965 Total unmethylated C's in Unknown context: 12034182 C methylated in CpG context: 11.5% C methylated in CHG context: 1.0% C methylated in CHH context: 1.0% C methylated in unknown context (CN or CHN): 3.2% Bismark completed in 0d 6h 8m 43s ==================== Bismark run complete ==================== Unable to flush stdout: Broken pipe