Job ID = 6367761 SRX = SRX4082375 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:32:50 prefetch.2.10.7: 1) Downloading 'SRR7164193'... 2020-06-15T23:32:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:35:40 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:35:41 prefetch.2.10.7: 'SRR7164193' is valid 2020-06-15T23:35:41 prefetch.2.10.7: 1) 'SRR7164193' was downloaded successfully 2020-06-15T23:35:41 prefetch.2.10.7: 'SRR7164193' has 0 unresolved dependencies Read 19591062 spots for SRR7164193/SRR7164193.sra Written 19591062 spots for SRR7164193/SRR7164193.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: 00:04:38 19591062 reads; of these: 19591062 (100.00%) were unpaired; of these: 244729 (1.25%) aligned 0 times 14611253 (74.58%) aligned exactly 1 time 4735080 (24.17%) aligned >1 times 98.75% overall alignment rate Time searching: 00:04:39 Overall time: 00:04:39 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] 3390530 / 19346333 = 0.1753 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 08:48:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082375/SRX4082375.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082375/SRX4082375.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082375/SRX4082375.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082375/SRX4082375.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 08:48:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:48:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:48:06: 1000000 INFO @ Tue, 16 Jun 2020 08:48:11: 2000000 INFO @ Tue, 16 Jun 2020 08:48:16: 3000000 INFO @ Tue, 16 Jun 2020 08:48:22: 4000000 INFO @ Tue, 16 Jun 2020 08:48:27: 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 08:48:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082375/SRX4082375.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082375/SRX4082375.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082375/SRX4082375.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082375/SRX4082375.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 08:48:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:48:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:48:32: 6000000 INFO @ Tue, 16 Jun 2020 08:48:36: 1000000 INFO @ Tue, 16 Jun 2020 08:48:38: 7000000 INFO @ Tue, 16 Jun 2020 08:48:42: 2000000 INFO @ Tue, 16 Jun 2020 08:48:43: 8000000 INFO @ Tue, 16 Jun 2020 08:48:48: 3000000 INFO @ Tue, 16 Jun 2020 08:48:49: 9000000 INFO @ Tue, 16 Jun 2020 08:48:53: 4000000 INFO @ Tue, 16 Jun 2020 08:48:54: 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 08:48:59: 5000000 INFO @ Tue, 16 Jun 2020 08:49:00: 11000000 INFO @ Tue, 16 Jun 2020 08:49:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082375/SRX4082375.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082375/SRX4082375.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082375/SRX4082375.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082375/SRX4082375.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 08:49:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:49:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:49:04: 6000000 INFO @ Tue, 16 Jun 2020 08:49:06: 12000000 INFO @ Tue, 16 Jun 2020 08:49:08: 1000000 INFO @ Tue, 16 Jun 2020 08:49:11: 7000000 INFO @ Tue, 16 Jun 2020 08:49:12: 13000000 INFO @ Tue, 16 Jun 2020 08:49:16: 2000000 INFO @ Tue, 16 Jun 2020 08:49:17: 8000000 INFO @ Tue, 16 Jun 2020 08:49:18: 14000000 INFO @ Tue, 16 Jun 2020 08:49:23: 3000000 INFO @ Tue, 16 Jun 2020 08:49:24: 9000000 INFO @ Tue, 16 Jun 2020 08:49:25: 15000000 INFO @ Tue, 16 Jun 2020 08:49:29: 4000000 INFO @ Tue, 16 Jun 2020 08:49:30: 10000000 INFO @ Tue, 16 Jun 2020 08:49:32: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 08:49:32: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 08:49:32: #1 total tags in treatment: 15955803 INFO @ Tue, 16 Jun 2020 08:49:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:49:32: #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 08:49:32: #1 tags after filtering in treatment: 15955803 INFO @ Tue, 16 Jun 2020 08:49:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:49:32: #1 finished! INFO @ Tue, 16 Jun 2020 08:49:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:49:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:49:33: #2 number of paired peaks: 392 WARNING @ Tue, 16 Jun 2020 08:49:33: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Tue, 16 Jun 2020 08:49:33: start model_add_line... INFO @ Tue, 16 Jun 2020 08:49:33: start X-correlation... INFO @ Tue, 16 Jun 2020 08:49:33: end of X-cor INFO @ Tue, 16 Jun 2020 08:49:33: #2 finished! INFO @ Tue, 16 Jun 2020 08:49:33: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:49:33: #2 alternative fragment length(s) may be 1,46,560 bps INFO @ Tue, 16 Jun 2020 08:49:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082375/SRX4082375.05_model.r WARNING @ Tue, 16 Jun 2020 08:49:33: #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 08:49:33: #2 You may need to consider one of the other alternative d(s): 1,46,560 WARNING @ Tue, 16 Jun 2020 08:49:33: #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 08:49:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:49:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:49:36: 11000000 INFO @ Tue, 16 Jun 2020 08:49:36: 5000000 INFO @ Tue, 16 Jun 2020 08:49:42: 12000000 INFO @ Tue, 16 Jun 2020 08:49:43: 6000000 INFO @ Tue, 16 Jun 2020 08:49:48: 13000000 INFO @ Tue, 16 Jun 2020 08:49:49: 7000000 INFO @ Tue, 16 Jun 2020 08:49:54: 14000000 INFO @ Tue, 16 Jun 2020 08:49:56: 8000000 INFO @ Tue, 16 Jun 2020 08:49:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:50:01: 15000000 INFO @ Tue, 16 Jun 2020 08:50:01: 9000000 INFO @ Tue, 16 Jun 2020 08:50:06: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 08:50:06: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 08:50:06: #1 total tags in treatment: 15955803 INFO @ Tue, 16 Jun 2020 08:50:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:06: #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 08:50:07: 10000000 INFO @ Tue, 16 Jun 2020 08:50:07: #1 tags after filtering in treatment: 15955803 INFO @ Tue, 16 Jun 2020 08:50:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:50:07: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:08: #2 number of paired peaks: 392 WARNING @ Tue, 16 Jun 2020 08:50:08: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Tue, 16 Jun 2020 08:50:08: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:08: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:08: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:08: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:08: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:50:08: #2 alternative fragment length(s) may be 1,46,560 bps INFO @ Tue, 16 Jun 2020 08:50:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082375/SRX4082375.10_model.r WARNING @ Tue, 16 Jun 2020 08:50:08: #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 08:50:08: #2 You may need to consider one of the other alternative d(s): 1,46,560 WARNING @ Tue, 16 Jun 2020 08:50:08: #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 08:50:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:50:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082375/SRX4082375.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:50:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082375/SRX4082375.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:50:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082375/SRX4082375.05_summits.bed INFO @ Tue, 16 Jun 2020 08:50:09: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:50:12: 11000000 INFO @ Tue, 16 Jun 2020 08:50:17: 12000000 INFO @ Tue, 16 Jun 2020 08:50:22: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:50:27: 14000000 INFO @ Tue, 16 Jun 2020 08:50:31: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:50:33: 15000000 INFO @ Tue, 16 Jun 2020 08:50:38: #1 tag size is determined as 49 bps INFO @ Tue, 16 Jun 2020 08:50:38: #1 tag size = 49 INFO @ Tue, 16 Jun 2020 08:50:38: #1 total tags in treatment: 15955803 INFO @ Tue, 16 Jun 2020 08:50:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:38: #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 08:50:38: #1 tags after filtering in treatment: 15955803 INFO @ Tue, 16 Jun 2020 08:50:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:50:38: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:39: #2 number of paired peaks: 392 WARNING @ Tue, 16 Jun 2020 08:50:39: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Tue, 16 Jun 2020 08:50:39: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:39: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:39: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:39: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:39: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:50:39: #2 alternative fragment length(s) may be 1,46,560 bps INFO @ Tue, 16 Jun 2020 08:50:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082375/SRX4082375.20_model.r WARNING @ Tue, 16 Jun 2020 08:50:39: #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 08:50:39: #2 You may need to consider one of the other alternative d(s): 1,46,560 WARNING @ Tue, 16 Jun 2020 08:50:39: #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 08:50:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:50:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082375/SRX4082375.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:50:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082375/SRX4082375.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:50:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082375/SRX4082375.10_summits.bed INFO @ Tue, 16 Jun 2020 08:50:43: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:51:02: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:51:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082375/SRX4082375.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:51:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082375/SRX4082375.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:51:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082375/SRX4082375.20_summits.bed INFO @ Tue, 16 Jun 2020 08:51:13: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling