/var/spool/slurm/d/job1239077/slurm_script: line 28: fg: no job control Begin flipping the strand of read 2 Wed Aug 28 10:15:39 2019 Input not indexed. Indexing... Wed Aug 28 10:20:46 2019 [E::fai_build3_core] Failed to open FASTA index /gscratch/srlab/sr320/data/geoduck/v074/Pgenerosa_v074.fa.fai : Permission denied [faidx] Could not build fai index /gscratch/srlab/sr320/data/geoduck/v074/Pgenerosa_v074.fa.fai Reference fasta not indexed. Indexing. Reference fasta wasn't indexed, and couldn't be indexed. Please try indexing it manually and running methylpy again. Begin flipping the strand of read 2 Wed Aug 28 10:21:11 2019 Input not indexed. Indexing... Wed Aug 28 10:27:24 2019 [E::fai_build3_core] Failed to open FASTA index /gscratch/srlab/sr320/data/geoduck/v074/Pgenerosa_v074.fa.fai : Permission denied [faidx] Could not build fai index /gscratch/srlab/sr320/data/geoduck/v074/Pgenerosa_v074.fa.fai Reference fasta not indexed. Indexing. Reference fasta wasn't indexed, and couldn't be indexed. Please try indexing it manually and running methylpy again. Begin flipping the strand of read 2 Wed Aug 28 10:27:54 2019 Input not indexed. Indexing... Wed Aug 28 10:32:37 2019 [E::fai_build3_core] Failed to open FASTA index /gscratch/srlab/sr320/data/geoduck/v074/Pgenerosa_v074.fa.fai : Permission denied [faidx] Could not build fai index /gscratch/srlab/sr320/data/geoduck/v074/Pgenerosa_v074.fa.fai Reference fasta not indexed. Indexing. Reference fasta wasn't indexed, and couldn't be indexed. Please try indexing it manually and running methylpy again. Begin flipping the strand of read 2 Wed Aug 28 10:33:01 2019 Input not indexed. Indexing... Wed Aug 28 10:37:44 2019 [E::fai_build3_core] Failed to open FASTA index /gscratch/srlab/sr320/data/geoduck/v074/Pgenerosa_v074.fa.fai : Permission denied [faidx] Could not build fai index /gscratch/srlab/sr320/data/geoduck/v074/Pgenerosa_v074.fa.fai Reference fasta not indexed. Indexing. Reference fasta wasn't indexed, and couldn't be indexed. Please try indexing it manually and running methylpy again. Begin flipping the strand of read 2 Wed Aug 28 10:38:09 2019 Input not indexed. Indexing... Wed Aug 28 10:41:36 2019 [E::fai_build3_core] Failed to open FASTA index /gscratch/srlab/sr320/data/geoduck/v074/Pgenerosa_v074.fa.fai : Permission denied [faidx] Could not build fai index /gscratch/srlab/sr320/data/geoduck/v074/Pgenerosa_v074.fa.fai Reference fasta not indexed. Indexing. Reference fasta wasn't indexed, and couldn't be indexed. Please try indexing it manually and running methylpy again. Begin flipping the strand of read 2 Wed Aug 28 10:41:55 2019 Input not indexed. Indexing... Wed Aug 28 10:47:43 2019 [E::fai_build3_core] Failed to open FASTA index /gscratch/srlab/sr320/data/geoduck/v074/Pgenerosa_v074.fa.fai : Permission denied [faidx] Could not build fai index /gscratch/srlab/sr320/data/geoduck/v074/Pgenerosa_v074.fa.fai Reference fasta not indexed. Indexing. Reference fasta wasn't indexed, and couldn't be indexed. Please try indexing it manually and running methylpy again. Begin flipping the strand of read 2 Wed Aug 28 10:48:12 2019 Input not indexed. Indexing... Wed Aug 28 10:52:44 2019 [E::fai_build3_core] Failed to open FASTA index /gscratch/srlab/sr320/data/geoduck/v074/Pgenerosa_v074.fa.fai : Permission denied [faidx] Could not build fai index /gscratch/srlab/sr320/data/geoduck/v074/Pgenerosa_v074.fa.fai Reference fasta not indexed. Indexing. Reference fasta wasn't indexed, and couldn't be indexed. Please try indexing it manually and running methylpy again. Begin flipping the strand of read 2 Wed Aug 28 10:53:08 2019 Input not indexed. Indexing... Wed Aug 28 10:57:35 2019 [E::fai_build3_core] Failed to open FASTA index /gscratch/srlab/sr320/data/geoduck/v074/Pgenerosa_v074.fa.fai : Permission denied [faidx] Could not build fai index /gscratch/srlab/sr320/data/geoduck/v074/Pgenerosa_v074.fa.fai Reference fasta not indexed. Indexing. Reference fasta wasn't indexed, and couldn't be indexed. Please try indexing it manually and running methylpy again. Begin flipping the strand of read 2 Wed Aug 28 10:57:58 2019 Input not indexed. Indexing... Wed Aug 28 11:03:21 2019 [E::fai_build3_core] Failed to open FASTA index /gscratch/srlab/sr320/data/geoduck/v074/Pgenerosa_v074.fa.fai : Permission denied [faidx] Could not build fai index /gscratch/srlab/sr320/data/geoduck/v074/Pgenerosa_v074.fa.fai Reference fasta not indexed. Indexing. Reference fasta wasn't indexed, and couldn't be indexed. Please try indexing it manually and running methylpy again. Begin flipping the strand of read 2 Wed Aug 28 11:03:47 2019 Input not indexed. Indexing... Wed Aug 28 11:08:12 2019 [E::fai_build3_core] Failed to open FASTA index /gscratch/srlab/sr320/data/geoduck/v074/Pgenerosa_v074.fa.fai : Permission denied [faidx] Could not build fai index /gscratch/srlab/sr320/data/geoduck/v074/Pgenerosa_v074.fa.fai Reference fasta not indexed. Indexing. Reference fasta wasn't indexed, and couldn't be indexed. Please try indexing it manually and running methylpy again. Begin flipping the strand of read 2 Wed Aug 28 11:08:36 2019 Input not indexed. Indexing... Wed Aug 28 11:13:14 2019 [E::fai_build3_core] Failed to open FASTA index /gscratch/srlab/sr320/data/geoduck/v074/Pgenerosa_v074.fa.fai : Permission denied [faidx] Could not build fai index /gscratch/srlab/sr320/data/geoduck/v074/Pgenerosa_v074.fa.fai Reference fasta not indexed. Indexing. Reference fasta wasn't indexed, and couldn't be indexed. Please try indexing it manually and running methylpy again. Begin flipping the strand of read 2 Wed Aug 28 11:13:37 2019 Input not indexed. Indexing... Wed Aug 28 11:18:48 2019 [E::fai_build3_core] Failed to open FASTA index /gscratch/srlab/sr320/data/geoduck/v074/Pgenerosa_v074.fa.fai : Permission denied [faidx] Could not build fai index /gscratch/srlab/sr320/data/geoduck/v074/Pgenerosa_v074.fa.fai Reference fasta not indexed. Indexing. Reference fasta wasn't indexed, and couldn't be indexed. Please try indexing it manually and running methylpy again. /var/spool/slurm/d/job1239077/slurm_script: line 40: fg: no job control Begin flipping the strand of read 2 Wed Aug 28 11:19:15 2019 Input not indexed. Indexing... Wed Aug 28 11:24:47 2019 [E::fai_build3_core] Failed to open FASTA index /gscratch/srlab/sr320/data/geoduck/v074/Pgenerosa_v074.fa.fai : Permission denied [faidx] Could not build fai index /gscratch/srlab/sr320/data/geoduck/v074/Pgenerosa_v074.fa.fai Reference fasta not indexed. Indexing. Reference fasta wasn't indexed, and couldn't be indexed. Please try indexing it manually and running methylpy again. Begin flipping the strand of read 2 Wed Aug 28 11:25:15 2019 slurmstepd: error: *** JOB 1239077 ON n2227 CANCELLED AT 2019-08-28T11:26:35 ***