Job ID = 6368804 SRX = SRX5709769 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:40:03 prefetch.2.10.7: 1) Downloading 'SRR8928719'... 2020-06-16T00:40:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:42:50 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:42:50 prefetch.2.10.7: 1) 'SRR8928719' was downloaded successfully 2020-06-16T00:42:50 prefetch.2.10.7: 'SRR8928719' has 0 unresolved dependencies Read 32921676 spots for SRR8928719/SRR8928719.sra Written 32921676 spots for SRR8928719/SRR8928719.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: 00:07:02 32921676 reads; of these: 32921676 (100.00%) were unpaired; of these: 5759998 (17.50%) aligned 0 times 22607552 (68.67%) aligned exactly 1 time 4554126 (13.83%) aligned >1 times 82.50% overall alignment rate Time searching: 00:07:02 Overall time: 00:07:02 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] 10165006 / 27161678 = 0.3742 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 09:58:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5709769/SRX5709769.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5709769/SRX5709769.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5709769/SRX5709769.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5709769/SRX5709769.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 09:58:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:58:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:58:59: 1000000 INFO @ Tue, 16 Jun 2020 09:59:07: 2000000 INFO @ Tue, 16 Jun 2020 09:59:14: 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 09:59:21: 4000000 INFO @ Tue, 16 Jun 2020 09:59:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5709769/SRX5709769.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5709769/SRX5709769.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5709769/SRX5709769.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5709769/SRX5709769.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 09:59:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:59:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:59:28: 5000000 INFO @ Tue, 16 Jun 2020 09:59:28: 1000000 INFO @ Tue, 16 Jun 2020 09:59:34: 2000000 INFO @ Tue, 16 Jun 2020 09:59:35: 6000000 INFO @ Tue, 16 Jun 2020 09:59:41: 3000000 INFO @ Tue, 16 Jun 2020 09:59:42: 7000000 INFO @ Tue, 16 Jun 2020 09:59:47: 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 09:59:49: 8000000 INFO @ Tue, 16 Jun 2020 09:59:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5709769/SRX5709769.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5709769/SRX5709769.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5709769/SRX5709769.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5709769/SRX5709769.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 09:59:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:59:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:59:54: 5000000 INFO @ Tue, 16 Jun 2020 09:59:57: 9000000 INFO @ Tue, 16 Jun 2020 09:59:59: 1000000 INFO @ Tue, 16 Jun 2020 10:00:02: 6000000 INFO @ Tue, 16 Jun 2020 10:00:04: 10000000 INFO @ Tue, 16 Jun 2020 10:00:06: 2000000 INFO @ Tue, 16 Jun 2020 10:00:09: 7000000 INFO @ Tue, 16 Jun 2020 10:00:11: 11000000 INFO @ Tue, 16 Jun 2020 10:00:14: 3000000 INFO @ Tue, 16 Jun 2020 10:00:17: 8000000 INFO @ Tue, 16 Jun 2020 10:00:19: 12000000 INFO @ Tue, 16 Jun 2020 10:00:21: 4000000 INFO @ Tue, 16 Jun 2020 10:00:24: 9000000 INFO @ Tue, 16 Jun 2020 10:00:26: 13000000 INFO @ Tue, 16 Jun 2020 10:00:28: 5000000 INFO @ Tue, 16 Jun 2020 10:00:31: 10000000 INFO @ Tue, 16 Jun 2020 10:00:34: 14000000 INFO @ Tue, 16 Jun 2020 10:00:36: 6000000 INFO @ Tue, 16 Jun 2020 10:00:38: 11000000 INFO @ Tue, 16 Jun 2020 10:00:41: 15000000 INFO @ Tue, 16 Jun 2020 10:00:43: 7000000 INFO @ Tue, 16 Jun 2020 10:00:45: 12000000 INFO @ Tue, 16 Jun 2020 10:00:48: 16000000 INFO @ Tue, 16 Jun 2020 10:00:50: 8000000 INFO @ Tue, 16 Jun 2020 10:00:53: 13000000 INFO @ Tue, 16 Jun 2020 10:00:55: #1 tag size is determined as 48 bps INFO @ Tue, 16 Jun 2020 10:00:55: #1 tag size = 48 INFO @ Tue, 16 Jun 2020 10:00:55: #1 total tags in treatment: 16996672 INFO @ Tue, 16 Jun 2020 10:00:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:00:55: #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 10:00:56: #1 tags after filtering in treatment: 16996672 INFO @ Tue, 16 Jun 2020 10:00:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:00:56: #1 finished! INFO @ Tue, 16 Jun 2020 10:00:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:00:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:00:57: #2 number of paired peaks: 357 WARNING @ Tue, 16 Jun 2020 10:00:57: Fewer paired peaks (357) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 357 pairs to build model! INFO @ Tue, 16 Jun 2020 10:00:57: start model_add_line... INFO @ Tue, 16 Jun 2020 10:00:57: start X-correlation... INFO @ Tue, 16 Jun 2020 10:00:57: end of X-cor INFO @ Tue, 16 Jun 2020 10:00:57: #2 finished! INFO @ Tue, 16 Jun 2020 10:00:57: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 10:00:57: #2 alternative fragment length(s) may be 1,24,579 bps INFO @ Tue, 16 Jun 2020 10:00:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5709769/SRX5709769.05_model.r WARNING @ Tue, 16 Jun 2020 10:00:57: #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 10:00:57: #2 You may need to consider one of the other alternative d(s): 1,24,579 WARNING @ Tue, 16 Jun 2020 10:00:57: #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 10:00:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:00:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:00:57: 9000000 INFO @ Tue, 16 Jun 2020 10:01:00: 14000000 INFO @ Tue, 16 Jun 2020 10:01:04: 10000000 INFO @ Tue, 16 Jun 2020 10:01:07: 15000000 INFO @ Tue, 16 Jun 2020 10:01:11: 11000000 INFO @ Tue, 16 Jun 2020 10:01:13: 16000000 INFO @ Tue, 16 Jun 2020 10:01:18: 12000000 INFO @ Tue, 16 Jun 2020 10:01:20: #1 tag size is determined as 48 bps INFO @ Tue, 16 Jun 2020 10:01:20: #1 tag size = 48 INFO @ Tue, 16 Jun 2020 10:01:20: #1 total tags in treatment: 16996672 INFO @ Tue, 16 Jun 2020 10:01:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:01:20: #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 10:01:21: #1 tags after filtering in treatment: 16996672 INFO @ Tue, 16 Jun 2020 10:01:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:01:21: #1 finished! INFO @ Tue, 16 Jun 2020 10:01:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:01:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:01:22: #2 number of paired peaks: 357 WARNING @ Tue, 16 Jun 2020 10:01:22: Fewer paired peaks (357) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 357 pairs to build model! INFO @ Tue, 16 Jun 2020 10:01:22: start model_add_line... INFO @ Tue, 16 Jun 2020 10:01:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:01:22: start X-correlation... INFO @ Tue, 16 Jun 2020 10:01:22: end of X-cor INFO @ Tue, 16 Jun 2020 10:01:22: #2 finished! INFO @ Tue, 16 Jun 2020 10:01:22: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 10:01:22: #2 alternative fragment length(s) may be 1,24,579 bps INFO @ Tue, 16 Jun 2020 10:01:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5709769/SRX5709769.10_model.r WARNING @ Tue, 16 Jun 2020 10:01:22: #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 10:01:22: #2 You may need to consider one of the other alternative d(s): 1,24,579 WARNING @ Tue, 16 Jun 2020 10:01:22: #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 10:01:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:01:22: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:01:24: 13000000 INFO @ Tue, 16 Jun 2020 10:01:31: 14000000 INFO @ Tue, 16 Jun 2020 10:01:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5709769/SRX5709769.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:01:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5709769/SRX5709769.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:01:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5709769/SRX5709769.05_summits.bed INFO @ Tue, 16 Jun 2020 10:01:34: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:01:37: 15000000 INFO @ Tue, 16 Jun 2020 10:01:43: 16000000 INFO @ Tue, 16 Jun 2020 10:01:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:01:50: #1 tag size is determined as 48 bps INFO @ Tue, 16 Jun 2020 10:01:50: #1 tag size = 48 INFO @ Tue, 16 Jun 2020 10:01:50: #1 total tags in treatment: 16996672 INFO @ Tue, 16 Jun 2020 10:01:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:01:50: #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 10:01:50: #1 tags after filtering in treatment: 16996672 INFO @ Tue, 16 Jun 2020 10:01:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:01:50: #1 finished! INFO @ Tue, 16 Jun 2020 10:01:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:01:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:01:51: #2 number of paired peaks: 357 WARNING @ Tue, 16 Jun 2020 10:01:51: Fewer paired peaks (357) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 357 pairs to build model! INFO @ Tue, 16 Jun 2020 10:01:51: start model_add_line... INFO @ Tue, 16 Jun 2020 10:01:51: start X-correlation... INFO @ Tue, 16 Jun 2020 10:01:51: end of X-cor INFO @ Tue, 16 Jun 2020 10:01:51: #2 finished! INFO @ Tue, 16 Jun 2020 10:01:51: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 10:01:51: #2 alternative fragment length(s) may be 1,24,579 bps INFO @ Tue, 16 Jun 2020 10:01:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5709769/SRX5709769.20_model.r WARNING @ Tue, 16 Jun 2020 10:01:51: #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 10:01:51: #2 You may need to consider one of the other alternative d(s): 1,24,579 WARNING @ Tue, 16 Jun 2020 10:01:51: #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 10:01:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:01:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:02:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5709769/SRX5709769.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:02:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5709769/SRX5709769.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:02:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5709769/SRX5709769.10_summits.bed INFO @ Tue, 16 Jun 2020 10:02:00: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:02:17: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:02:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5709769/SRX5709769.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:02:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5709769/SRX5709769.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:02:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5709769/SRX5709769.20_summits.bed INFO @ Tue, 16 Jun 2020 10:02:29: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling