Job ID = 6367895 SRX = SRX4194184 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:42:59 prefetch.2.10.7: 1) Downloading 'SRR7291437'... 2020-06-15T23:42:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:44:06 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:44:06 prefetch.2.10.7: 'SRR7291437' is valid 2020-06-15T23:44:06 prefetch.2.10.7: 1) 'SRR7291437' was downloaded successfully 2020-06-15T23:44:06 prefetch.2.10.7: 'SRR7291437' has 0 unresolved dependencies Read 7493038 spots for SRR7291437/SRR7291437.sra Written 7493038 spots for SRR7291437/SRR7291437.sra 2020-06-15T23:44:44 prefetch.2.10.7: 1) Downloading 'SRR7291438'... 2020-06-15T23:44:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:46:07 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:46:07 prefetch.2.10.7: 'SRR7291438' is valid 2020-06-15T23:46:07 prefetch.2.10.7: 1) 'SRR7291438' was downloaded successfully 2020-06-15T23:46:07 prefetch.2.10.7: 'SRR7291438' has 0 unresolved dependencies Read 7336373 spots for SRR7291438/SRR7291438.sra Written 7336373 spots for SRR7291438/SRR7291438.sra 2020-06-15T23:46:48 prefetch.2.10.7: 1) Downloading 'SRR7291439'... 2020-06-15T23:46:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:48:09 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:48:09 prefetch.2.10.7: 'SRR7291439' is valid 2020-06-15T23:48:09 prefetch.2.10.7: 1) 'SRR7291439' was downloaded successfully 2020-06-15T23:48:09 prefetch.2.10.7: 'SRR7291439' has 0 unresolved dependencies Read 7480446 spots for SRR7291439/SRR7291439.sra Written 7480446 spots for SRR7291439/SRR7291439.sra 2020-06-15T23:48:48 prefetch.2.10.7: 1) Downloading 'SRR7291440'... 2020-06-15T23:48:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:50:08 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:50:08 prefetch.2.10.7: 'SRR7291440' is valid 2020-06-15T23:50:08 prefetch.2.10.7: 1) 'SRR7291440' was downloaded successfully 2020-06-15T23:50:08 prefetch.2.10.7: 'SRR7291440' has 0 unresolved dependencies Read 7251348 spots for SRR7291440/SRR7291440.sra Written 7251348 spots for SRR7291440/SRR7291440.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: 00:13:27 29561205 reads; of these: 29561205 (100.00%) were unpaired; of these: 649920 (2.20%) aligned 0 times 20734525 (70.14%) aligned exactly 1 time 8176760 (27.66%) aligned >1 times 97.80% overall alignment rate Time searching: 00:13:27 Overall time: 00:13:27 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] 10623740 / 28911285 = 0.3675 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 09:12:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194184/SRX4194184.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194184/SRX4194184.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194184/SRX4194184.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194184/SRX4194184.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 09:12:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:12:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:13:02: 1000000 INFO @ Tue, 16 Jun 2020 09:13:09: 2000000 INFO @ Tue, 16 Jun 2020 09:13:16: 3000000 INFO @ Tue, 16 Jun 2020 09:13:23: 4000000 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 09:13:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194184/SRX4194184.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194184/SRX4194184.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194184/SRX4194184.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194184/SRX4194184.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 09:13:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:13:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:13:31: 5000000 INFO @ Tue, 16 Jun 2020 09:13:33: 1000000 INFO @ Tue, 16 Jun 2020 09:13:38: 6000000 INFO @ Tue, 16 Jun 2020 09:13:41: 2000000 INFO @ Tue, 16 Jun 2020 09:13:46: 7000000 INFO @ Tue, 16 Jun 2020 09:13:49: 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 09:13:54: 8000000 INFO @ Tue, 16 Jun 2020 09:13:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194184/SRX4194184.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194184/SRX4194184.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194184/SRX4194184.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194184/SRX4194184.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 09:13:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:13:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:13:56: 4000000 INFO @ Tue, 16 Jun 2020 09:14:02: 9000000 INFO @ Tue, 16 Jun 2020 09:14:04: 1000000 INFO @ Tue, 16 Jun 2020 09:14:05: 5000000 INFO @ Tue, 16 Jun 2020 09:14:10: 10000000 INFO @ Tue, 16 Jun 2020 09:14:12: 2000000 INFO @ Tue, 16 Jun 2020 09:14:13: 6000000 INFO @ Tue, 16 Jun 2020 09:14:18: 11000000 INFO @ Tue, 16 Jun 2020 09:14:20: 3000000 INFO @ Tue, 16 Jun 2020 09:14:21: 7000000 INFO @ Tue, 16 Jun 2020 09:14:26: 12000000 INFO @ Tue, 16 Jun 2020 09:14:28: 4000000 INFO @ Tue, 16 Jun 2020 09:14:29: 8000000 INFO @ Tue, 16 Jun 2020 09:14:34: 13000000 INFO @ Tue, 16 Jun 2020 09:14:36: 5000000 INFO @ Tue, 16 Jun 2020 09:14:37: 9000000 INFO @ Tue, 16 Jun 2020 09:14:42: 14000000 INFO @ Tue, 16 Jun 2020 09:14:44: 6000000 INFO @ Tue, 16 Jun 2020 09:14:45: 10000000 INFO @ Tue, 16 Jun 2020 09:14:50: 15000000 INFO @ Tue, 16 Jun 2020 09:14:52: 7000000 INFO @ Tue, 16 Jun 2020 09:14:53: 11000000 INFO @ Tue, 16 Jun 2020 09:14:58: 16000000 INFO @ Tue, 16 Jun 2020 09:15:00: 8000000 INFO @ Tue, 16 Jun 2020 09:15:00: 12000000 INFO @ Tue, 16 Jun 2020 09:15:05: 17000000 INFO @ Tue, 16 Jun 2020 09:15:08: 9000000 INFO @ Tue, 16 Jun 2020 09:15:08: 13000000 INFO @ Tue, 16 Jun 2020 09:15:13: 18000000 INFO @ Tue, 16 Jun 2020 09:15:15: 10000000 INFO @ Tue, 16 Jun 2020 09:15:16: #1 tag size is determined as 58 bps INFO @ Tue, 16 Jun 2020 09:15:16: #1 tag size = 58 INFO @ Tue, 16 Jun 2020 09:15:16: #1 total tags in treatment: 18287545 INFO @ Tue, 16 Jun 2020 09:15:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:15:16: #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 09:15:16: 14000000 INFO @ Tue, 16 Jun 2020 09:15:16: #1 tags after filtering in treatment: 18287545 INFO @ Tue, 16 Jun 2020 09:15:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:15:16: #1 finished! INFO @ Tue, 16 Jun 2020 09:15:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:15:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:15:17: #2 number of paired peaks: 658 WARNING @ Tue, 16 Jun 2020 09:15:17: Fewer paired peaks (658) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 658 pairs to build model! INFO @ Tue, 16 Jun 2020 09:15:17: start model_add_line... INFO @ Tue, 16 Jun 2020 09:15:17: start X-correlation... INFO @ Tue, 16 Jun 2020 09:15:17: end of X-cor INFO @ Tue, 16 Jun 2020 09:15:17: #2 finished! INFO @ Tue, 16 Jun 2020 09:15:17: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:15:17: #2 alternative fragment length(s) may be 1,37 bps INFO @ Tue, 16 Jun 2020 09:15:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194184/SRX4194184.05_model.r WARNING @ Tue, 16 Jun 2020 09:15:17: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:15:17: #2 You may need to consider one of the other alternative d(s): 1,37 WARNING @ Tue, 16 Jun 2020 09:15:17: #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 09:15:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:15:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:15:23: 15000000 INFO @ Tue, 16 Jun 2020 09:15:23: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:15:31: 16000000 INFO @ Tue, 16 Jun 2020 09:15:31: 12000000 INFO @ Tue, 16 Jun 2020 09:15:38: 17000000 INFO @ Tue, 16 Jun 2020 09:15:39: 13000000 INFO @ Tue, 16 Jun 2020 09:15:46: 18000000 INFO @ Tue, 16 Jun 2020 09:15:46: 14000000 INFO @ Tue, 16 Jun 2020 09:15:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:15:48: #1 tag size is determined as 58 bps INFO @ Tue, 16 Jun 2020 09:15:48: #1 tag size = 58 INFO @ Tue, 16 Jun 2020 09:15:48: #1 total tags in treatment: 18287545 INFO @ Tue, 16 Jun 2020 09:15:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:15:48: #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 09:15:48: #1 tags after filtering in treatment: 18287545 INFO @ Tue, 16 Jun 2020 09:15:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:15:48: #1 finished! INFO @ Tue, 16 Jun 2020 09:15:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:15:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:15:49: #2 number of paired peaks: 658 WARNING @ Tue, 16 Jun 2020 09:15:49: Fewer paired peaks (658) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 658 pairs to build model! INFO @ Tue, 16 Jun 2020 09:15:49: start model_add_line... INFO @ Tue, 16 Jun 2020 09:15:50: start X-correlation... INFO @ Tue, 16 Jun 2020 09:15:50: end of X-cor INFO @ Tue, 16 Jun 2020 09:15:50: #2 finished! INFO @ Tue, 16 Jun 2020 09:15:50: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:15:50: #2 alternative fragment length(s) may be 1,37 bps INFO @ Tue, 16 Jun 2020 09:15:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194184/SRX4194184.10_model.r WARNING @ Tue, 16 Jun 2020 09:15:50: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:15:50: #2 You may need to consider one of the other alternative d(s): 1,37 WARNING @ Tue, 16 Jun 2020 09:15:50: #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 09:15:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:15:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:15:53: 15000000 INFO @ Tue, 16 Jun 2020 09:16:00: 16000000 INFO @ Tue, 16 Jun 2020 09:16:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194184/SRX4194184.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:16:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194184/SRX4194184.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:16:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194184/SRX4194184.05_summits.bed INFO @ Tue, 16 Jun 2020 09:16:00: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:16:07: 17000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:16:14: 18000000 INFO @ Tue, 16 Jun 2020 09:16:16: #1 tag size is determined as 58 bps INFO @ Tue, 16 Jun 2020 09:16:16: #1 tag size = 58 INFO @ Tue, 16 Jun 2020 09:16:16: #1 total tags in treatment: 18287545 INFO @ Tue, 16 Jun 2020 09:16:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:16:16: #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 09:16:16: #1 tags after filtering in treatment: 18287545 INFO @ Tue, 16 Jun 2020 09:16:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:16:16: #1 finished! INFO @ Tue, 16 Jun 2020 09:16:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:16:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:16:17: #2 number of paired peaks: 658 WARNING @ Tue, 16 Jun 2020 09:16:17: Fewer paired peaks (658) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 658 pairs to build model! INFO @ Tue, 16 Jun 2020 09:16:17: start model_add_line... INFO @ Tue, 16 Jun 2020 09:16:17: start X-correlation... INFO @ Tue, 16 Jun 2020 09:16:17: end of X-cor INFO @ Tue, 16 Jun 2020 09:16:17: #2 finished! INFO @ Tue, 16 Jun 2020 09:16:17: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:16:17: #2 alternative fragment length(s) may be 1,37 bps INFO @ Tue, 16 Jun 2020 09:16:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194184/SRX4194184.20_model.r WARNING @ Tue, 16 Jun 2020 09:16:17: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:16:17: #2 You may need to consider one of the other alternative d(s): 1,37 WARNING @ Tue, 16 Jun 2020 09:16:17: #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 09:16:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:16:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:16:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:16:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194184/SRX4194184.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:16:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194184/SRX4194184.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:16:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194184/SRX4194184.10_summits.bed INFO @ Tue, 16 Jun 2020 09:16:31: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:16:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:16:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194184/SRX4194184.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:16:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194184/SRX4194184.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:16:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194184/SRX4194184.20_summits.bed INFO @ Tue, 16 Jun 2020 09:16:59: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling