Job ID = 6367900 SRX = SRX4194191 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:45:59 prefetch.2.10.7: 1) Downloading 'SRR7291458'... 2020-06-15T23:45:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:47:36 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:47:36 prefetch.2.10.7: 'SRR7291458' is valid 2020-06-15T23:47:36 prefetch.2.10.7: 1) 'SRR7291458' was downloaded successfully 2020-06-15T23:47:36 prefetch.2.10.7: 'SRR7291458' has 0 unresolved dependencies Read 5561597 spots for SRR7291458/SRR7291458.sra Written 5561597 spots for SRR7291458/SRR7291458.sra 2020-06-15T23:48:10 prefetch.2.10.7: 1) Downloading 'SRR7291459'... 2020-06-15T23:48:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:50:27 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:50:28 prefetch.2.10.7: 'SRR7291459' is valid 2020-06-15T23:50:28 prefetch.2.10.7: 1) 'SRR7291459' was downloaded successfully 2020-06-15T23:50:28 prefetch.2.10.7: 'SRR7291459' has 0 unresolved dependencies Read 5451568 spots for SRR7291459/SRR7291459.sra Written 5451568 spots for SRR7291459/SRR7291459.sra 2020-06-15T23:50:58 prefetch.2.10.7: 1) Downloading 'SRR7291460'... 2020-06-15T23:50:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:51:53 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:51:53 prefetch.2.10.7: 'SRR7291460' is valid 2020-06-15T23:51:53 prefetch.2.10.7: 1) 'SRR7291460' was downloaded successfully 2020-06-15T23:51:53 prefetch.2.10.7: 'SRR7291460' has 0 unresolved dependencies Read 5560025 spots for SRR7291460/SRR7291460.sra Written 5560025 spots for SRR7291460/SRR7291460.sra 2020-06-15T23:52:27 prefetch.2.10.7: 1) Downloading 'SRR7291461'... 2020-06-15T23:52:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:53:10 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:53:11 prefetch.2.10.7: 'SRR7291461' is valid 2020-06-15T23:53:11 prefetch.2.10.7: 1) 'SRR7291461' was downloaded successfully 2020-06-15T23:53:11 prefetch.2.10.7: 'SRR7291461' has 0 unresolved dependencies Read 5386837 spots for SRR7291461/SRR7291461.sra Written 5386837 spots for SRR7291461/SRR7291461.sra 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: 00:09:15 21960027 reads; of these: 21960027 (100.00%) were unpaired; of these: 557424 (2.54%) aligned 0 times 15998127 (72.85%) aligned exactly 1 time 5404476 (24.61%) aligned >1 times 97.46% overall alignment rate Time searching: 00:09:15 Overall time: 00:09:15 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 5348564 / 21402603 = 0.2499 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:09:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194191/SRX4194191.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194191/SRX4194191.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194191/SRX4194191.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194191/SRX4194191.bam'] # control file = None # effective genome size = 9.00e+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 @ Tue, 16 Jun 2020 09:09:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:52: 1000000 INFO @ Tue, 16 Jun 2020 09:10:00: 2000000 INFO @ Tue, 16 Jun 2020 09:10:08: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:10:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194191/SRX4194191.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194191/SRX4194191.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194191/SRX4194191.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194191/SRX4194191.bam'] # control file = None # effective genome size = 9.00e+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 @ Tue, 16 Jun 2020 09:10:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:16: 4000000 INFO @ Tue, 16 Jun 2020 09:10:22: 1000000 INFO @ Tue, 16 Jun 2020 09:10:25: 5000000 INFO @ Tue, 16 Jun 2020 09:10:30: 2000000 INFO @ Tue, 16 Jun 2020 09:10:33: 6000000 INFO @ Tue, 16 Jun 2020 09:10:38: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:10:42: 7000000 INFO @ Tue, 16 Jun 2020 09:10:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194191/SRX4194191.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194191/SRX4194191.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194191/SRX4194191.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194191/SRX4194191.bam'] # control file = None # effective genome size = 9.00e+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 @ Tue, 16 Jun 2020 09:10:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:46: 4000000 INFO @ Tue, 16 Jun 2020 09:10:50: 8000000 INFO @ Tue, 16 Jun 2020 09:10:53: 1000000 INFO @ Tue, 16 Jun 2020 09:10:55: 5000000 INFO @ Tue, 16 Jun 2020 09:10:58: 9000000 INFO @ Tue, 16 Jun 2020 09:11:01: 2000000 INFO @ Tue, 16 Jun 2020 09:11:03: 6000000 INFO @ Tue, 16 Jun 2020 09:11:06: 10000000 INFO @ Tue, 16 Jun 2020 09:11:09: 3000000 INFO @ Tue, 16 Jun 2020 09:11:11: 7000000 INFO @ Tue, 16 Jun 2020 09:11:14: 11000000 INFO @ Tue, 16 Jun 2020 09:11:17: 4000000 INFO @ Tue, 16 Jun 2020 09:11:19: 8000000 INFO @ Tue, 16 Jun 2020 09:11:22: 12000000 INFO @ Tue, 16 Jun 2020 09:11:24: 5000000 INFO @ Tue, 16 Jun 2020 09:11:27: 9000000 INFO @ Tue, 16 Jun 2020 09:11:30: 13000000 INFO @ Tue, 16 Jun 2020 09:11:32: 6000000 INFO @ Tue, 16 Jun 2020 09:11:35: 10000000 INFO @ Tue, 16 Jun 2020 09:11:38: 14000000 INFO @ Tue, 16 Jun 2020 09:11:40: 7000000 INFO @ Tue, 16 Jun 2020 09:11:43: 11000000 INFO @ Tue, 16 Jun 2020 09:11:46: 15000000 INFO @ Tue, 16 Jun 2020 09:11:47: 8000000 INFO @ Tue, 16 Jun 2020 09:11:50: 12000000 INFO @ Tue, 16 Jun 2020 09:11:54: 16000000 INFO @ Tue, 16 Jun 2020 09:11:54: #1 tag size is determined as 71 bps INFO @ Tue, 16 Jun 2020 09:11:54: #1 tag size = 71 INFO @ Tue, 16 Jun 2020 09:11:54: #1 total tags in treatment: 16054039 INFO @ Tue, 16 Jun 2020 09:11:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:11:54: #1 tags after filtering in treatment: 16054039 INFO @ Tue, 16 Jun 2020 09:11:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:11:54: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:55: 9000000 INFO @ Tue, 16 Jun 2020 09:11:55: #2 number of paired peaks: 557 WARNING @ Tue, 16 Jun 2020 09:11:55: Fewer paired peaks (557) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 557 pairs to build model! INFO @ Tue, 16 Jun 2020 09:11:55: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:56: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:56: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:56: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:56: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:11:56: #2 alternative fragment length(s) may be 2,32,52 bps INFO @ Tue, 16 Jun 2020 09:11:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194191/SRX4194191.05_model.r WARNING @ Tue, 16 Jun 2020 09:11:56: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:11:56: #2 You may need to consider one of the other alternative d(s): 2,32,52 WARNING @ Tue, 16 Jun 2020 09:11:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:11:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:11:58: 13000000 INFO @ Tue, 16 Jun 2020 09:12:02: 10000000 INFO @ Tue, 16 Jun 2020 09:12:06: 14000000 INFO @ Tue, 16 Jun 2020 09:12:10: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:12:14: 15000000 INFO @ Tue, 16 Jun 2020 09:12:18: 12000000 INFO @ Tue, 16 Jun 2020 09:12:21: 16000000 INFO @ Tue, 16 Jun 2020 09:12:22: #1 tag size is determined as 71 bps INFO @ Tue, 16 Jun 2020 09:12:22: #1 tag size = 71 INFO @ Tue, 16 Jun 2020 09:12:22: #1 total tags in treatment: 16054039 INFO @ Tue, 16 Jun 2020 09:12:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:12:22: #1 tags after filtering in treatment: 16054039 INFO @ Tue, 16 Jun 2020 09:12:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:22: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:23: #2 number of paired peaks: 557 WARNING @ Tue, 16 Jun 2020 09:12:23: Fewer paired peaks (557) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 557 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:23: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:23: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:23: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:23: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:23: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:12:23: #2 alternative fragment length(s) may be 2,32,52 bps INFO @ Tue, 16 Jun 2020 09:12:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194191/SRX4194191.10_model.r WARNING @ Tue, 16 Jun 2020 09:12:23: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:12:23: #2 You may need to consider one of the other alternative d(s): 2,32,52 WARNING @ Tue, 16 Jun 2020 09:12:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:12:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:25: 13000000 INFO @ Tue, 16 Jun 2020 09:12:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:32: 14000000 INFO @ Tue, 16 Jun 2020 09:12:39: 15000000 INFO @ Tue, 16 Jun 2020 09:12:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194191/SRX4194191.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194191/SRX4194191.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194191/SRX4194191.05_summits.bed INFO @ Tue, 16 Jun 2020 09:12:40: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:12:45: 16000000 INFO @ Tue, 16 Jun 2020 09:12:46: #1 tag size is determined as 71 bps INFO @ Tue, 16 Jun 2020 09:12:46: #1 tag size = 71 INFO @ Tue, 16 Jun 2020 09:12:46: #1 total tags in treatment: 16054039 INFO @ Tue, 16 Jun 2020 09:12:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:12:46: #1 tags after filtering in treatment: 16054039 INFO @ Tue, 16 Jun 2020 09:12:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:46: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:47: #2 number of paired peaks: 557 WARNING @ Tue, 16 Jun 2020 09:12:47: Fewer paired peaks (557) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 557 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:47: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:47: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:47: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:47: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:47: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:12:47: #2 alternative fragment length(s) may be 2,32,52 bps INFO @ Tue, 16 Jun 2020 09:12:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194191/SRX4194191.20_model.r WARNING @ Tue, 16 Jun 2020 09:12:47: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:12:47: #2 You may need to consider one of the other alternative d(s): 2,32,52 WARNING @ Tue, 16 Jun 2020 09:12:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:12:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:47: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:12:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:13:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194191/SRX4194191.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194191/SRX4194191.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194191/SRX4194191.10_summits.bed INFO @ Tue, 16 Jun 2020 09:13:07: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:13:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:13:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194191/SRX4194191.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194191/SRX4194191.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194191/SRX4194191.20_summits.bed INFO @ Tue, 16 Jun 2020 09:13:30: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling