Job ID = 6368791 SRX = SRX5702598 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:26:05 prefetch.2.10.7: 1) Downloading 'SRR8921276'... 2020-06-16T00:26:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:27:20 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:27:20 prefetch.2.10.7: 'SRR8921276' is valid 2020-06-16T00:27:20 prefetch.2.10.7: 1) 'SRR8921276' was downloaded successfully 2020-06-16T00:27:20 prefetch.2.10.7: 'SRR8921276' has 0 unresolved dependencies Read 21994809 spots for SRR8921276/SRR8921276.sra Written 21994809 spots for SRR8921276/SRR8921276.sra 2020-06-16T00:28:42 prefetch.2.10.7: 1) Downloading 'SRR8921277'... 2020-06-16T00:28:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:33:57 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:33:57 prefetch.2.10.7: 1) 'SRR8921277' was downloaded successfully 2020-06-16T00:33:57 prefetch.2.10.7: 'SRR8921277' has 0 unresolved dependencies Read 39096930 spots for SRR8921277/SRR8921277.sra Written 39096930 spots for SRR8921277/SRR8921277.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:56 61091739 reads; of these: 61091739 (100.00%) were unpaired; of these: 28779366 (47.11%) aligned 0 times 25525764 (41.78%) aligned exactly 1 time 6786609 (11.11%) aligned >1 times 52.89% overall alignment rate Time searching: 00:11:57 Overall time: 00:11:57 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 16 files... [bam_rmdupse_core] 18419700 / 32312373 = 0.5701 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 09:55:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5702598/SRX5702598.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5702598/SRX5702598.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5702598/SRX5702598.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5702598/SRX5702598.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 09:55:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:55:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:55:15: 1000000 INFO @ Tue, 16 Jun 2020 09:55:21: 2000000 INFO @ Tue, 16 Jun 2020 09:55:27: 3000000 INFO @ Tue, 16 Jun 2020 09:55:32: 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 09:55:38: 5000000 INFO @ Tue, 16 Jun 2020 09:55:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5702598/SRX5702598.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5702598/SRX5702598.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5702598/SRX5702598.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5702598/SRX5702598.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 09:55:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:55:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:55:44: 6000000 INFO @ Tue, 16 Jun 2020 09:55:45: 1000000 INFO @ Tue, 16 Jun 2020 09:55:51: 7000000 INFO @ Tue, 16 Jun 2020 09:55:51: 2000000 INFO @ Tue, 16 Jun 2020 09:55:57: 8000000 INFO @ Tue, 16 Jun 2020 09:55:58: 3000000 INFO @ Tue, 16 Jun 2020 09:56:04: 9000000 INFO @ Tue, 16 Jun 2020 09:56:04: 4000000 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 09:56:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5702598/SRX5702598.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5702598/SRX5702598.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5702598/SRX5702598.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5702598/SRX5702598.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 09:56:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:56:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:56:10: 10000000 INFO @ Tue, 16 Jun 2020 09:56:11: 5000000 INFO @ Tue, 16 Jun 2020 09:56:15: 1000000 INFO @ Tue, 16 Jun 2020 09:56:16: 11000000 INFO @ Tue, 16 Jun 2020 09:56:17: 6000000 INFO @ Tue, 16 Jun 2020 09:56:22: 2000000 INFO @ Tue, 16 Jun 2020 09:56:23: 12000000 INFO @ Tue, 16 Jun 2020 09:56:24: 7000000 INFO @ Tue, 16 Jun 2020 09:56:28: 3000000 INFO @ Tue, 16 Jun 2020 09:56:29: 13000000 INFO @ Tue, 16 Jun 2020 09:56:30: 8000000 INFO @ Tue, 16 Jun 2020 09:56:35: 4000000 INFO @ Tue, 16 Jun 2020 09:56:35: #1 tag size is determined as 57 bps INFO @ Tue, 16 Jun 2020 09:56:35: #1 tag size = 57 INFO @ Tue, 16 Jun 2020 09:56:35: #1 total tags in treatment: 13892673 INFO @ Tue, 16 Jun 2020 09:56:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:56:35: #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 09:56:35: #1 tags after filtering in treatment: 13892673 INFO @ Tue, 16 Jun 2020 09:56:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:56:35: #1 finished! INFO @ Tue, 16 Jun 2020 09:56:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:56:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:56:36: #2 number of paired peaks: 319 WARNING @ Tue, 16 Jun 2020 09:56:36: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Tue, 16 Jun 2020 09:56:36: start model_add_line... INFO @ Tue, 16 Jun 2020 09:56:36: 9000000 INFO @ Tue, 16 Jun 2020 09:56:36: start X-correlation... INFO @ Tue, 16 Jun 2020 09:56:37: end of X-cor INFO @ Tue, 16 Jun 2020 09:56:37: #2 finished! INFO @ Tue, 16 Jun 2020 09:56:37: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:56:37: #2 alternative fragment length(s) may be 2,12,38,565 bps INFO @ Tue, 16 Jun 2020 09:56:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5702598/SRX5702598.05_model.r WARNING @ Tue, 16 Jun 2020 09:56:37: #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 09:56:37: #2 You may need to consider one of the other alternative d(s): 2,12,38,565 WARNING @ Tue, 16 Jun 2020 09:56:37: #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 09:56:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:56:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:56:41: 5000000 INFO @ Tue, 16 Jun 2020 09:56:43: 10000000 INFO @ Tue, 16 Jun 2020 09:56:48: 6000000 INFO @ Tue, 16 Jun 2020 09:56:49: 11000000 INFO @ Tue, 16 Jun 2020 09:56:54: 7000000 INFO @ Tue, 16 Jun 2020 09:56:56: 12000000 INFO @ Tue, 16 Jun 2020 09:57:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:57:01: 8000000 INFO @ Tue, 16 Jun 2020 09:57:02: 13000000 INFO @ Tue, 16 Jun 2020 09:57:07: 9000000 INFO @ Tue, 16 Jun 2020 09:57:08: #1 tag size is determined as 57 bps INFO @ Tue, 16 Jun 2020 09:57:08: #1 tag size = 57 INFO @ Tue, 16 Jun 2020 09:57:08: #1 total tags in treatment: 13892673 INFO @ Tue, 16 Jun 2020 09:57:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:57:08: #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 09:57:08: #1 tags after filtering in treatment: 13892673 INFO @ Tue, 16 Jun 2020 09:57:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:57:08: #1 finished! INFO @ Tue, 16 Jun 2020 09:57:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:57:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:57:09: #2 number of paired peaks: 319 WARNING @ Tue, 16 Jun 2020 09:57:09: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Tue, 16 Jun 2020 09:57:09: start model_add_line... INFO @ Tue, 16 Jun 2020 09:57:09: start X-correlation... INFO @ Tue, 16 Jun 2020 09:57:09: end of X-cor INFO @ Tue, 16 Jun 2020 09:57:09: #2 finished! INFO @ Tue, 16 Jun 2020 09:57:09: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:57:09: #2 alternative fragment length(s) may be 2,12,38,565 bps INFO @ Tue, 16 Jun 2020 09:57:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5702598/SRX5702598.10_model.r WARNING @ Tue, 16 Jun 2020 09:57:09: #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 09:57:09: #2 You may need to consider one of the other alternative d(s): 2,12,38,565 WARNING @ Tue, 16 Jun 2020 09:57:09: #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 09:57:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:57:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:57:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5702598/SRX5702598.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:57:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5702598/SRX5702598.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:57:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5702598/SRX5702598.05_summits.bed INFO @ Tue, 16 Jun 2020 09:57:12: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:57:13: 10000000 INFO @ Tue, 16 Jun 2020 09:57:19: 11000000 INFO @ Tue, 16 Jun 2020 09:57:24: 12000000 INFO @ Tue, 16 Jun 2020 09:57:30: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:57:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:57:35: #1 tag size is determined as 57 bps INFO @ Tue, 16 Jun 2020 09:57:35: #1 tag size = 57 INFO @ Tue, 16 Jun 2020 09:57:35: #1 total tags in treatment: 13892673 INFO @ Tue, 16 Jun 2020 09:57:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:57:35: #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 09:57:35: #1 tags after filtering in treatment: 13892673 INFO @ Tue, 16 Jun 2020 09:57:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:57:35: #1 finished! INFO @ Tue, 16 Jun 2020 09:57:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:57:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:57:36: #2 number of paired peaks: 319 WARNING @ Tue, 16 Jun 2020 09:57:36: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Tue, 16 Jun 2020 09:57:36: start model_add_line... INFO @ Tue, 16 Jun 2020 09:57:36: start X-correlation... INFO @ Tue, 16 Jun 2020 09:57:36: end of X-cor INFO @ Tue, 16 Jun 2020 09:57:36: #2 finished! INFO @ Tue, 16 Jun 2020 09:57:36: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 09:57:36: #2 alternative fragment length(s) may be 2,12,38,565 bps INFO @ Tue, 16 Jun 2020 09:57:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5702598/SRX5702598.20_model.r WARNING @ Tue, 16 Jun 2020 09:57:36: #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 09:57:36: #2 You may need to consider one of the other alternative d(s): 2,12,38,565 WARNING @ Tue, 16 Jun 2020 09:57:36: #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 09:57:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:57:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:57:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5702598/SRX5702598.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:57:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5702598/SRX5702598.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:57:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5702598/SRX5702598.10_summits.bed INFO @ Tue, 16 Jun 2020 09:57:44: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:58:00: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:58:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5702598/SRX5702598.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:58:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5702598/SRX5702598.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:58:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5702598/SRX5702598.20_summits.bed INFO @ Tue, 16 Jun 2020 09:58:11: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling