Job ID = 14519946 SRX = SRX10341702 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-01-15T09:25:55 fastq-dump.2.10.7 err: transfer canceled while allocating buffer within file system module - Cannot KHttpFileTimedReadChunked: to=480 2022-01-15T09:25:55 fastq-dump.2.10.7 err: data corrupt while selecting function within transform module - failed SRR13963710/SRR13963710.sra ============================================================= An error occurred during processing. A report was generated into the file '/home/okishinya/ncbi_error_report.txt'. If the problem persists, you may consider sending the file to 'sra-tools@ncbi.nlm.nih.gov' for assistance. ============================================================= fastq-dump quit with error code 3 fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:36 4419584 reads; of these: 4419584 (100.00%) were unpaired; of these: 97 (0.00%) aligned 0 times 4037203 (91.35%) aligned exactly 1 time 382284 (8.65%) aligned >1 times 100.00% overall alignment rate Time searching: 00:00:36 Overall time: 00:00:36 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 1576258 / 4419487 = 0.3567 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 18:29:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10341702/SRX10341702.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10341702/SRX10341702.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10341702/SRX10341702.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10341702/SRX10341702.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 15 Jan 2022 18:29:08: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:29:08: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:29:13: 1000000 INFO @ Sat, 15 Jan 2022 18:29:18: 2000000 INFO @ Sat, 15 Jan 2022 18:29:23: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 18:29:23: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 18:29:23: #1 total tags in treatment: 2843229 INFO @ Sat, 15 Jan 2022 18:29:23: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:29:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 18:29:23: #1 tags after filtering in treatment: 2843228 INFO @ Sat, 15 Jan 2022 18:29:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 18:29:23: #1 finished! INFO @ Sat, 15 Jan 2022 18:29:23: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:29:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:29:23: #2 number of paired peaks: 1218 INFO @ Sat, 15 Jan 2022 18:29:23: start model_add_line... INFO @ Sat, 15 Jan 2022 18:29:23: start X-correlation... INFO @ Sat, 15 Jan 2022 18:29:23: end of X-cor INFO @ Sat, 15 Jan 2022 18:29:23: #2 finished! INFO @ Sat, 15 Jan 2022 18:29:23: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 18:29:23: #2 alternative fragment length(s) may be 0,21,24,52,85,137,154,158,175,189,208,237,266,283,329,350,487,515,547,579 bps INFO @ Sat, 15 Jan 2022 18:29:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10341702/SRX10341702.05_model.r WARNING @ Sat, 15 Jan 2022 18:29:23: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 18:29:23: #2 You may need to consider one of the other alternative d(s): 0,21,24,52,85,137,154,158,175,189,208,237,266,283,329,350,487,515,547,579 WARNING @ Sat, 15 Jan 2022 18:29:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 18:29:23: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:29:23: #3 Pre-compute pvalue-qvalue table... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 18:29:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10341702/SRX10341702.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10341702/SRX10341702.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10341702/SRX10341702.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10341702/SRX10341702.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 15 Jan 2022 18:29:38: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:29:38: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:29:43: 1000000 INFO @ Sat, 15 Jan 2022 18:29:48: 2000000 INFO @ Sat, 15 Jan 2022 18:29:53: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 18:29:53: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 18:29:53: #1 total tags in treatment: 2843229 INFO @ Sat, 15 Jan 2022 18:29:53: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:29:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 18:29:53: #1 tags after filtering in treatment: 2843228 INFO @ Sat, 15 Jan 2022 18:29:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 18:29:53: #1 finished! INFO @ Sat, 15 Jan 2022 18:29:53: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:29:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:29:53: #2 number of paired peaks: 1218 INFO @ Sat, 15 Jan 2022 18:29:53: start model_add_line... INFO @ Sat, 15 Jan 2022 18:29:53: start X-correlation... INFO @ Sat, 15 Jan 2022 18:29:53: end of X-cor INFO @ Sat, 15 Jan 2022 18:29:53: #2 finished! INFO @ Sat, 15 Jan 2022 18:29:53: #2 predicted fragment length is 0 bps INFO @ Sat, 15 Jan 2022 18:29:53: #2 alternative fragment length(s) may be 0,21,24,52,85,137,154,158,175,189,208,237,266,283,329,350,487,515,547,579 bps INFO @ Sat, 15 Jan 2022 18:29:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX10341702/SRX10341702.10_model.r WARNING @ Sat, 15 Jan 2022 18:29:53: #2 Since the d (0) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 18:29:53: #2 You may need to consider one of the other alternative d(s): 0,21,24,52,85,137,154,158,175,189,208,237,266,283,329,350,487,515,547,579 WARNING @ Sat, 15 Jan 2022 18:29:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 18:29:53: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:29:53: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 18:30:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX10341702/SRX10341702.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX10341702/SRX10341702.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX10341702/SRX10341702.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX10341702/SRX10341702.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Sat, 15 Jan 2022 18:30:08: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:30:08: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:30:13: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 /var/spool/uge/at149/job_scripts/14519946: line 297: 17889 Terminated MACS $i /var/spool/uge/at149/job_scripts/14519946: line 297: 18038 Terminated MACS $i /var/spool/uge/at149/job_scripts/14519946: line 297: 19216 Terminated MACS $i ls: cannot access SRX10341702.05.bed: No such file or directory mv: cannot stat ‘SRX10341702.05.bed’: No such file or directory mv: cannot stat ‘SRX10341702.05.bb’: No such file or directory ls: cannot access SRX10341702.10.bed: No such file or directory mv: cannot stat ‘SRX10341702.10.bed’: No such file or directory mv: cannot stat ‘SRX10341702.10.bb’: No such file or directory ls: cannot access SRX10341702.20.bed: No such file or directory mv: cannot stat ‘SRX10341702.20.bed’: No such file or directory mv: cannot stat ‘SRX10341702.20.bb’: No such file or directory