Job ID = 6368783 SRX = SRX5702590 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:25:34 prefetch.2.10.7: 1) Downloading 'SRR8921259'... 2020-06-16T00:25:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:27:05 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:27:06 prefetch.2.10.7: 'SRR8921259' is valid 2020-06-16T00:27:06 prefetch.2.10.7: 1) 'SRR8921259' was downloaded successfully 2020-06-16T00:27:06 prefetch.2.10.7: 'SRR8921259' has 0 unresolved dependencies Read 25796593 spots for SRR8921259/SRR8921259.sra Written 25796593 spots for SRR8921259/SRR8921259.sra 2020-06-16T00:28:41 prefetch.2.10.7: 1) Downloading 'SRR8921260'... 2020-06-16T00:28:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:29:53 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:29:54 prefetch.2.10.7: 'SRR8921260' is valid 2020-06-16T00:29:54 prefetch.2.10.7: 1) 'SRR8921260' was downloaded successfully 2020-06-16T00:29:54 prefetch.2.10.7: 'SRR8921260' has 0 unresolved dependencies Read 20784388 spots for SRR8921260/SRR8921260.sra Written 20784388 spots for SRR8921260/SRR8921260.sra 2020-06-16T00:31:11 prefetch.2.10.7: 1) Downloading 'SRR8921261'... 2020-06-16T00:31:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:35:34 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:35:34 prefetch.2.10.7: 1) 'SRR8921261' was downloaded successfully 2020-06-16T00:35:34 prefetch.2.10.7: 'SRR8921261' has 0 unresolved dependencies Read 49989487 spots for SRR8921261/SRR8921261.sra Written 49989487 spots for SRR8921261/SRR8921261.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: 00:21:48 96570468 reads; of these: 96570468 (100.00%) were unpaired; of these: 30114683 (31.18%) aligned 0 times 52046336 (53.89%) aligned exactly 1 time 14409449 (14.92%) aligned >1 times 68.82% overall alignment rate Time searching: 00:21:48 Overall time: 00:21:48 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 28 files... [bam_rmdupse_core] 41238184 / 66455785 = 0.6205 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 10:14:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5702590/SRX5702590.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5702590/SRX5702590.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5702590/SRX5702590.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5702590/SRX5702590.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 10:14:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:14:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:14:39: 1000000 INFO @ Tue, 16 Jun 2020 10:14:45: 2000000 INFO @ Tue, 16 Jun 2020 10:14:50: 3000000 INFO @ Tue, 16 Jun 2020 10:14:55: 4000000 INFO @ Tue, 16 Jun 2020 10:15:01: 5000000 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 10:15:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5702590/SRX5702590.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5702590/SRX5702590.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5702590/SRX5702590.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5702590/SRX5702590.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 10:15:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:15:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:15:06: 6000000 INFO @ Tue, 16 Jun 2020 10:15:10: 1000000 INFO @ Tue, 16 Jun 2020 10:15:12: 7000000 INFO @ Tue, 16 Jun 2020 10:15:15: 2000000 INFO @ Tue, 16 Jun 2020 10:15:18: 8000000 INFO @ Tue, 16 Jun 2020 10:15:21: 3000000 INFO @ Tue, 16 Jun 2020 10:15:23: 9000000 INFO @ Tue, 16 Jun 2020 10:15:27: 4000000 INFO @ Tue, 16 Jun 2020 10:15:29: 10000000 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 10:15:32: 5000000 INFO @ Tue, 16 Jun 2020 10:15:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5702590/SRX5702590.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5702590/SRX5702590.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5702590/SRX5702590.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5702590/SRX5702590.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 10:15:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:15:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:15:34: 11000000 INFO @ Tue, 16 Jun 2020 10:15:38: 6000000 INFO @ Tue, 16 Jun 2020 10:15:40: 1000000 INFO @ Tue, 16 Jun 2020 10:15:40: 12000000 INFO @ Tue, 16 Jun 2020 10:15:44: 7000000 INFO @ Tue, 16 Jun 2020 10:15:45: 2000000 INFO @ Tue, 16 Jun 2020 10:15:46: 13000000 INFO @ Tue, 16 Jun 2020 10:15:50: 8000000 INFO @ Tue, 16 Jun 2020 10:15:51: 3000000 INFO @ Tue, 16 Jun 2020 10:15:52: 14000000 INFO @ Tue, 16 Jun 2020 10:15:55: 9000000 INFO @ Tue, 16 Jun 2020 10:15:57: 4000000 INFO @ Tue, 16 Jun 2020 10:15:57: 15000000 INFO @ Tue, 16 Jun 2020 10:16:01: 10000000 INFO @ Tue, 16 Jun 2020 10:16:03: 5000000 INFO @ Tue, 16 Jun 2020 10:16:03: 16000000 INFO @ Tue, 16 Jun 2020 10:16:07: 11000000 INFO @ Tue, 16 Jun 2020 10:16:08: 6000000 INFO @ Tue, 16 Jun 2020 10:16:09: 17000000 INFO @ Tue, 16 Jun 2020 10:16:13: 12000000 INFO @ Tue, 16 Jun 2020 10:16:14: 7000000 INFO @ Tue, 16 Jun 2020 10:16:15: 18000000 INFO @ Tue, 16 Jun 2020 10:16:18: 13000000 INFO @ Tue, 16 Jun 2020 10:16:20: 8000000 INFO @ Tue, 16 Jun 2020 10:16:20: 19000000 INFO @ Tue, 16 Jun 2020 10:16:24: 14000000 INFO @ Tue, 16 Jun 2020 10:16:26: 9000000 INFO @ Tue, 16 Jun 2020 10:16:26: 20000000 INFO @ Tue, 16 Jun 2020 10:16:30: 15000000 INFO @ Tue, 16 Jun 2020 10:16:31: 10000000 INFO @ Tue, 16 Jun 2020 10:16:32: 21000000 INFO @ Tue, 16 Jun 2020 10:16:36: 16000000 INFO @ Tue, 16 Jun 2020 10:16:37: 11000000 INFO @ Tue, 16 Jun 2020 10:16:37: 22000000 INFO @ Tue, 16 Jun 2020 10:16:41: 17000000 INFO @ Tue, 16 Jun 2020 10:16:42: 12000000 INFO @ Tue, 16 Jun 2020 10:16:43: 23000000 INFO @ Tue, 16 Jun 2020 10:16:47: 18000000 INFO @ Tue, 16 Jun 2020 10:16:48: 13000000 INFO @ Tue, 16 Jun 2020 10:16:49: 24000000 INFO @ Tue, 16 Jun 2020 10:16:53: 19000000 INFO @ Tue, 16 Jun 2020 10:16:54: 14000000 INFO @ Tue, 16 Jun 2020 10:16:54: 25000000 INFO @ Tue, 16 Jun 2020 10:16:56: #1 tag size is determined as 58 bps INFO @ Tue, 16 Jun 2020 10:16:56: #1 tag size = 58 INFO @ Tue, 16 Jun 2020 10:16:56: #1 total tags in treatment: 25217601 INFO @ Tue, 16 Jun 2020 10:16:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:16:56: #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 10:16:56: #1 tags after filtering in treatment: 25217601 INFO @ Tue, 16 Jun 2020 10:16:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:16:56: #1 finished! INFO @ Tue, 16 Jun 2020 10:16:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:16:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:16:58: #2 number of paired peaks: 183 WARNING @ Tue, 16 Jun 2020 10:16:58: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Tue, 16 Jun 2020 10:16:58: start model_add_line... INFO @ Tue, 16 Jun 2020 10:16:58: start X-correlation... INFO @ Tue, 16 Jun 2020 10:16:58: end of X-cor INFO @ Tue, 16 Jun 2020 10:16:58: #2 finished! INFO @ Tue, 16 Jun 2020 10:16:58: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 10:16:58: #2 alternative fragment length(s) may be 1,28,43,561 bps INFO @ Tue, 16 Jun 2020 10:16:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5702590/SRX5702590.05_model.r WARNING @ Tue, 16 Jun 2020 10:16:58: #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 10:16:58: #2 You may need to consider one of the other alternative d(s): 1,28,43,561 WARNING @ Tue, 16 Jun 2020 10:16:58: #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 10:16:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:16:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:16:58: 20000000 INFO @ Tue, 16 Jun 2020 10:17:00: 15000000 INFO @ Tue, 16 Jun 2020 10:17:04: 21000000 INFO @ Tue, 16 Jun 2020 10:17:05: 16000000 INFO @ Tue, 16 Jun 2020 10:17:10: 22000000 INFO @ Tue, 16 Jun 2020 10:17:11: 17000000 INFO @ Tue, 16 Jun 2020 10:17:15: 23000000 INFO @ Tue, 16 Jun 2020 10:17:17: 18000000 INFO @ Tue, 16 Jun 2020 10:17:21: 24000000 INFO @ Tue, 16 Jun 2020 10:17:22: 19000000 INFO @ Tue, 16 Jun 2020 10:17:27: 25000000 INFO @ Tue, 16 Jun 2020 10:17:28: 20000000 INFO @ Tue, 16 Jun 2020 10:17:28: #1 tag size is determined as 58 bps INFO @ Tue, 16 Jun 2020 10:17:28: #1 tag size = 58 INFO @ Tue, 16 Jun 2020 10:17:28: #1 total tags in treatment: 25217601 INFO @ Tue, 16 Jun 2020 10:17:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:17:28: #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 10:17:29: #1 tags after filtering in treatment: 25217601 INFO @ Tue, 16 Jun 2020 10:17:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:17:29: #1 finished! INFO @ Tue, 16 Jun 2020 10:17:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:17:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:17:31: #2 number of paired peaks: 183 WARNING @ Tue, 16 Jun 2020 10:17:31: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Tue, 16 Jun 2020 10:17:31: start model_add_line... INFO @ Tue, 16 Jun 2020 10:17:31: start X-correlation... INFO @ Tue, 16 Jun 2020 10:17:31: end of X-cor INFO @ Tue, 16 Jun 2020 10:17:31: #2 finished! INFO @ Tue, 16 Jun 2020 10:17:31: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 10:17:31: #2 alternative fragment length(s) may be 1,28,43,561 bps INFO @ Tue, 16 Jun 2020 10:17:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5702590/SRX5702590.10_model.r WARNING @ Tue, 16 Jun 2020 10:17:31: #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 10:17:31: #2 You may need to consider one of the other alternative d(s): 1,28,43,561 WARNING @ Tue, 16 Jun 2020 10:17:31: #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 10:17:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:17:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:17:33: 21000000 INFO @ Tue, 16 Jun 2020 10:17:35: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:17:39: 22000000 INFO @ Tue, 16 Jun 2020 10:17:44: 23000000 INFO @ Tue, 16 Jun 2020 10:17:50: 24000000 INFO @ Tue, 16 Jun 2020 10:17:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5702590/SRX5702590.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:17:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5702590/SRX5702590.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:17:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5702590/SRX5702590.05_summits.bed INFO @ Tue, 16 Jun 2020 10:17:52: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:17:55: 25000000 INFO @ Tue, 16 Jun 2020 10:17:57: #1 tag size is determined as 58 bps INFO @ Tue, 16 Jun 2020 10:17:57: #1 tag size = 58 INFO @ Tue, 16 Jun 2020 10:17:57: #1 total tags in treatment: 25217601 INFO @ Tue, 16 Jun 2020 10:17:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:17:57: #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 10:17:57: #1 tags after filtering in treatment: 25217601 INFO @ Tue, 16 Jun 2020 10:17:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:17:57: #1 finished! INFO @ Tue, 16 Jun 2020 10:17:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:17:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:17:59: #2 number of paired peaks: 183 WARNING @ Tue, 16 Jun 2020 10:17:59: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Tue, 16 Jun 2020 10:17:59: start model_add_line... INFO @ Tue, 16 Jun 2020 10:17:59: start X-correlation... INFO @ Tue, 16 Jun 2020 10:17:59: end of X-cor INFO @ Tue, 16 Jun 2020 10:17:59: #2 finished! INFO @ Tue, 16 Jun 2020 10:17:59: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 10:17:59: #2 alternative fragment length(s) may be 1,28,43,561 bps INFO @ Tue, 16 Jun 2020 10:17:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5702590/SRX5702590.20_model.r WARNING @ Tue, 16 Jun 2020 10:17:59: #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 10:17:59: #2 You may need to consider one of the other alternative d(s): 1,28,43,561 WARNING @ Tue, 16 Jun 2020 10:17:59: #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 10:17:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:17:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:18:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:18:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5702590/SRX5702590.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:18:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5702590/SRX5702590.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:18:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5702590/SRX5702590.10_summits.bed INFO @ Tue, 16 Jun 2020 10:18:25: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:18:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:18:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5702590/SRX5702590.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:18:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5702590/SRX5702590.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:18:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5702590/SRX5702590.20_summits.bed INFO @ Tue, 16 Jun 2020 10:18:53: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling