Job ID = 6367042 SRX = SRX2761387 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:18:31 prefetch.2.10.7: 1) Downloading 'SRR5476961'... 2020-06-15T23:18:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:21:20 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:21:20 prefetch.2.10.7: 1) 'SRR5476961' was downloaded successfully Read 17943886 spots for SRR5476961/SRR5476961.sra Written 17943886 spots for SRR5476961/SRR5476961.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: 00:04:04 17943886 reads; of these: 17943886 (100.00%) were unpaired; of these: 840670 (4.68%) aligned 0 times 13798247 (76.90%) aligned exactly 1 time 3304969 (18.42%) aligned >1 times 95.32% overall alignment rate Time searching: 00:04:04 Overall time: 00:04:04 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 8 files... [bam_rmdupse_core] 1629473 / 17103216 = 0.0953 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 08:30:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2761387/SRX2761387.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2761387/SRX2761387.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2761387/SRX2761387.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2761387/SRX2761387.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 08:30:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:30:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:30:57: 1000000 INFO @ Tue, 16 Jun 2020 08:31:02: 2000000 INFO @ Tue, 16 Jun 2020 08:31:08: 3000000 INFO @ Tue, 16 Jun 2020 08:31:13: 4000000 INFO @ Tue, 16 Jun 2020 08:31:18: 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 08:31:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2761387/SRX2761387.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2761387/SRX2761387.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2761387/SRX2761387.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2761387/SRX2761387.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 08:31:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:24: 6000000 INFO @ Tue, 16 Jun 2020 08:31:28: 1000000 INFO @ Tue, 16 Jun 2020 08:31:30: 7000000 INFO @ Tue, 16 Jun 2020 08:31:34: 2000000 INFO @ Tue, 16 Jun 2020 08:31:35: 8000000 INFO @ Tue, 16 Jun 2020 08:31:40: 3000000 INFO @ Tue, 16 Jun 2020 08:31:41: 9000000 INFO @ Tue, 16 Jun 2020 08:31:46: 4000000 INFO @ Tue, 16 Jun 2020 08:31:47: 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 08:31:52: 5000000 INFO @ Tue, 16 Jun 2020 08:31:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2761387/SRX2761387.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2761387/SRX2761387.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2761387/SRX2761387.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2761387/SRX2761387.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 08:31:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:31:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:31:53: 11000000 INFO @ Tue, 16 Jun 2020 08:31:58: 6000000 INFO @ Tue, 16 Jun 2020 08:31:58: 1000000 INFO @ Tue, 16 Jun 2020 08:31:59: 12000000 INFO @ Tue, 16 Jun 2020 08:32:04: 7000000 INFO @ Tue, 16 Jun 2020 08:32:04: 2000000 INFO @ Tue, 16 Jun 2020 08:32:05: 13000000 INFO @ Tue, 16 Jun 2020 08:32:10: 8000000 INFO @ Tue, 16 Jun 2020 08:32:11: 3000000 INFO @ Tue, 16 Jun 2020 08:32:11: 14000000 INFO @ Tue, 16 Jun 2020 08:32:16: 9000000 INFO @ Tue, 16 Jun 2020 08:32:17: 4000000 INFO @ Tue, 16 Jun 2020 08:32:17: 15000000 INFO @ Tue, 16 Jun 2020 08:32:20: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:32:20: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:32:20: #1 total tags in treatment: 15473743 INFO @ Tue, 16 Jun 2020 08:32:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:32:20: #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 08:32:20: #1 tags after filtering in treatment: 15473743 INFO @ Tue, 16 Jun 2020 08:32:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:32:20: #1 finished! INFO @ Tue, 16 Jun 2020 08:32:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:32:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:32:21: #2 number of paired peaks: 386 WARNING @ Tue, 16 Jun 2020 08:32:21: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Tue, 16 Jun 2020 08:32:21: start model_add_line... INFO @ Tue, 16 Jun 2020 08:32:22: start X-correlation... INFO @ Tue, 16 Jun 2020 08:32:22: end of X-cor INFO @ Tue, 16 Jun 2020 08:32:22: #2 finished! INFO @ Tue, 16 Jun 2020 08:32:22: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:32:22: #2 alternative fragment length(s) may be 1,20,45 bps INFO @ Tue, 16 Jun 2020 08:32:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2761387/SRX2761387.05_model.r WARNING @ Tue, 16 Jun 2020 08:32:22: #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 08:32:22: #2 You may need to consider one of the other alternative d(s): 1,20,45 WARNING @ Tue, 16 Jun 2020 08:32:22: #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 08:32:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:32:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:32:22: 10000000 INFO @ Tue, 16 Jun 2020 08:32:23: 5000000 INFO @ Tue, 16 Jun 2020 08:32:29: 11000000 INFO @ Tue, 16 Jun 2020 08:32:29: 6000000 INFO @ Tue, 16 Jun 2020 08:32:35: 12000000 INFO @ Tue, 16 Jun 2020 08:32:35: 7000000 INFO @ Tue, 16 Jun 2020 08:32:41: 13000000 INFO @ Tue, 16 Jun 2020 08:32:41: 8000000 INFO @ Tue, 16 Jun 2020 08:32:47: 14000000 INFO @ Tue, 16 Jun 2020 08:32:47: 9000000 INFO @ Tue, 16 Jun 2020 08:32:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:32:53: 15000000 INFO @ Tue, 16 Jun 2020 08:32:53: 10000000 INFO @ Tue, 16 Jun 2020 08:32:56: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:32:56: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:32:56: #1 total tags in treatment: 15473743 INFO @ Tue, 16 Jun 2020 08:32:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:32:56: #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 08:32:56: #1 tags after filtering in treatment: 15473743 INFO @ Tue, 16 Jun 2020 08:32:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:32:56: #1 finished! INFO @ Tue, 16 Jun 2020 08:32:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:32:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:32:57: #2 number of paired peaks: 386 WARNING @ Tue, 16 Jun 2020 08:32:57: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Tue, 16 Jun 2020 08:32:57: start model_add_line... INFO @ Tue, 16 Jun 2020 08:32:57: start X-correlation... INFO @ Tue, 16 Jun 2020 08:32:57: end of X-cor INFO @ Tue, 16 Jun 2020 08:32:57: #2 finished! INFO @ Tue, 16 Jun 2020 08:32:57: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:32:57: #2 alternative fragment length(s) may be 1,20,45 bps INFO @ Tue, 16 Jun 2020 08:32:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2761387/SRX2761387.10_model.r WARNING @ Tue, 16 Jun 2020 08:32:57: #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 08:32:57: #2 You may need to consider one of the other alternative d(s): 1,20,45 WARNING @ Tue, 16 Jun 2020 08:32:57: #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 08:32:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:32:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:32:59: 11000000 INFO @ Tue, 16 Jun 2020 08:33:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2761387/SRX2761387.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:33:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2761387/SRX2761387.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:33:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2761387/SRX2761387.05_summits.bed INFO @ Tue, 16 Jun 2020 08:33:03: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:33:05: 12000000 INFO @ Tue, 16 Jun 2020 08:33:11: 13000000 INFO @ Tue, 16 Jun 2020 08:33:16: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:33:22: 15000000 INFO @ Tue, 16 Jun 2020 08:33:24: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:33:24: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:33:24: #1 total tags in treatment: 15473743 INFO @ Tue, 16 Jun 2020 08:33:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:33:24: #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 08:33:24: #1 tags after filtering in treatment: 15473743 INFO @ Tue, 16 Jun 2020 08:33:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:33:24: #1 finished! INFO @ Tue, 16 Jun 2020 08:33:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:33:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:33:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:33:25: #2 number of paired peaks: 386 WARNING @ Tue, 16 Jun 2020 08:33:25: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Tue, 16 Jun 2020 08:33:25: start model_add_line... INFO @ Tue, 16 Jun 2020 08:33:26: start X-correlation... INFO @ Tue, 16 Jun 2020 08:33:26: end of X-cor INFO @ Tue, 16 Jun 2020 08:33:26: #2 finished! INFO @ Tue, 16 Jun 2020 08:33:26: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:33:26: #2 alternative fragment length(s) may be 1,20,45 bps INFO @ Tue, 16 Jun 2020 08:33:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2761387/SRX2761387.20_model.r WARNING @ Tue, 16 Jun 2020 08:33:26: #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 08:33:26: #2 You may need to consider one of the other alternative d(s): 1,20,45 WARNING @ Tue, 16 Jun 2020 08:33:26: #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 08:33:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:33:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:33:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2761387/SRX2761387.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:33:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2761387/SRX2761387.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:33:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2761387/SRX2761387.10_summits.bed INFO @ Tue, 16 Jun 2020 08:33:37: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:33:52: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:34:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2761387/SRX2761387.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:34:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2761387/SRX2761387.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:34:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2761387/SRX2761387.20_summits.bed INFO @ Tue, 16 Jun 2020 08:34:05: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling