Job ID = 8070251 SRX = SRX7217780 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 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: 00:11:57 7231417 reads; of these: 7231417 (100.00%) were paired; of these: 1925310 (26.62%) aligned concordantly 0 times 4562395 (63.09%) aligned concordantly exactly 1 time 743712 (10.28%) aligned concordantly >1 times ---- 1925310 pairs aligned concordantly 0 times; of these: 605833 (31.47%) aligned discordantly 1 time ---- 1319477 pairs aligned 0 times concordantly or discordantly; of these: 2638954 mates make up the pairs; of these: 2402937 (91.06%) aligned 0 times 121439 (4.60%) aligned exactly 1 time 114578 (4.34%) aligned >1 times 83.39% 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 12 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 924433 / 5872820 = 0.1574 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 @ Sat, 08 Aug 2020 13:18:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7217780/SRX7217780.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7217780/SRX7217780.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7217780/SRX7217780.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7217780/SRX7217780.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 @ Sat, 08 Aug 2020 13:18:31: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:18:31: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:18:40: 1000000 INFO @ Sat, 08 Aug 2020 13:18:48: 2000000 INFO @ Sat, 08 Aug 2020 13:18:56: 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 @ Sat, 08 Aug 2020 13:19:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7217780/SRX7217780.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7217780/SRX7217780.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7217780/SRX7217780.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7217780/SRX7217780.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 @ Sat, 08 Aug 2020 13:19:01: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:19:01: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:19:05: 4000000 INFO @ Sat, 08 Aug 2020 13:19:12: 1000000 INFO @ Sat, 08 Aug 2020 13:19:15: 5000000 INFO @ Sat, 08 Aug 2020 13:19:24: 2000000 INFO @ Sat, 08 Aug 2020 13:19:24: 6000000 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 @ Sat, 08 Aug 2020 13:19:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7217780/SRX7217780.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7217780/SRX7217780.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7217780/SRX7217780.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7217780/SRX7217780.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 @ Sat, 08 Aug 2020 13:19:31: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:19:31: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:19:34: 7000000 INFO @ Sat, 08 Aug 2020 13:19:35: 3000000 INFO @ Sat, 08 Aug 2020 13:19:41: 1000000 INFO @ Sat, 08 Aug 2020 13:19:44: 8000000 INFO @ Sat, 08 Aug 2020 13:19:47: 4000000 INFO @ Sat, 08 Aug 2020 13:19:51: 2000000 INFO @ Sat, 08 Aug 2020 13:19:54: 9000000 INFO @ Sat, 08 Aug 2020 13:19:58: 5000000 INFO @ Sat, 08 Aug 2020 13:20:01: 3000000 INFO @ Sat, 08 Aug 2020 13:20:04: 10000000 INFO @ Sat, 08 Aug 2020 13:20:06: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:20:06: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:20:06: #1 total tags in treatment: 4460389 INFO @ Sat, 08 Aug 2020 13:20:06: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:20:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:20:07: #1 tags after filtering in treatment: 4109005 INFO @ Sat, 08 Aug 2020 13:20:07: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 13:20:07: #1 finished! INFO @ Sat, 08 Aug 2020 13:20:07: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:20:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:20:07: #2 number of paired peaks: 397 WARNING @ Sat, 08 Aug 2020 13:20:07: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Sat, 08 Aug 2020 13:20:07: start model_add_line... INFO @ Sat, 08 Aug 2020 13:20:07: start X-correlation... INFO @ Sat, 08 Aug 2020 13:20:07: end of X-cor INFO @ Sat, 08 Aug 2020 13:20:07: #2 finished! INFO @ Sat, 08 Aug 2020 13:20:07: #2 predicted fragment length is 203 bps INFO @ Sat, 08 Aug 2020 13:20:07: #2 alternative fragment length(s) may be 203 bps INFO @ Sat, 08 Aug 2020 13:20:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7217780/SRX7217780.05_model.r WARNING @ Sat, 08 Aug 2020 13:20:07: #2 Since the d (203) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:20:07: #2 You may need to consider one of the other alternative d(s): 203 WARNING @ Sat, 08 Aug 2020 13:20:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 13:20:07: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:20:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:20:09: 6000000 INFO @ Sat, 08 Aug 2020 13:20:11: 4000000 INFO @ Sat, 08 Aug 2020 13:20:16: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:20:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7217780/SRX7217780.05_peaks.xls INFO @ Sat, 08 Aug 2020 13:20:20: 7000000 INFO @ Sat, 08 Aug 2020 13:20:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7217780/SRX7217780.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:20:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7217780/SRX7217780.05_summits.bed INFO @ Sat, 08 Aug 2020 13:20:20: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (310 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:20:21: 5000000 INFO @ Sat, 08 Aug 2020 13:20:31: 6000000 INFO @ Sat, 08 Aug 2020 13:20:31: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 13:20:41: 7000000 INFO @ Sat, 08 Aug 2020 13:20:42: 9000000 INFO @ Sat, 08 Aug 2020 13:20:50: 8000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:20:53: 10000000 INFO @ Sat, 08 Aug 2020 13:20:55: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:20:55: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:20:55: #1 total tags in treatment: 4460389 INFO @ Sat, 08 Aug 2020 13:20:55: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:20:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:20:55: #1 tags after filtering in treatment: 4109005 INFO @ Sat, 08 Aug 2020 13:20:55: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 13:20:55: #1 finished! INFO @ Sat, 08 Aug 2020 13:20:55: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:20:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:20:56: #2 number of paired peaks: 397 WARNING @ Sat, 08 Aug 2020 13:20:56: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Sat, 08 Aug 2020 13:20:56: start model_add_line... INFO @ Sat, 08 Aug 2020 13:20:56: start X-correlation... INFO @ Sat, 08 Aug 2020 13:20:56: end of X-cor INFO @ Sat, 08 Aug 2020 13:20:56: #2 finished! INFO @ Sat, 08 Aug 2020 13:20:56: #2 predicted fragment length is 203 bps INFO @ Sat, 08 Aug 2020 13:20:56: #2 alternative fragment length(s) may be 203 bps INFO @ Sat, 08 Aug 2020 13:20:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7217780/SRX7217780.10_model.r WARNING @ Sat, 08 Aug 2020 13:20:56: #2 Since the d (203) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:20:56: #2 You may need to consider one of the other alternative d(s): 203 WARNING @ Sat, 08 Aug 2020 13:20:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 13:20:56: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:20:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:21:00: 9000000 INFO @ Sat, 08 Aug 2020 13:21:05: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:21:09: 10000000 INFO @ Sat, 08 Aug 2020 13:21:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7217780/SRX7217780.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:21:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7217780/SRX7217780.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:21:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7217780/SRX7217780.10_summits.bed INFO @ Sat, 08 Aug 2020 13:21:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (219 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:21:10: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:21:10: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:21:10: #1 total tags in treatment: 4460389 INFO @ Sat, 08 Aug 2020 13:21:10: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:21:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:21:10: #1 tags after filtering in treatment: 4109005 INFO @ Sat, 08 Aug 2020 13:21:10: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 13:21:10: #1 finished! INFO @ Sat, 08 Aug 2020 13:21:10: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:21:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:21:11: #2 number of paired peaks: 397 WARNING @ Sat, 08 Aug 2020 13:21:11: Fewer paired peaks (397) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 397 pairs to build model! INFO @ Sat, 08 Aug 2020 13:21:11: start model_add_line... INFO @ Sat, 08 Aug 2020 13:21:11: start X-correlation... INFO @ Sat, 08 Aug 2020 13:21:11: end of X-cor INFO @ Sat, 08 Aug 2020 13:21:11: #2 finished! INFO @ Sat, 08 Aug 2020 13:21:11: #2 predicted fragment length is 203 bps INFO @ Sat, 08 Aug 2020 13:21:11: #2 alternative fragment length(s) may be 203 bps INFO @ Sat, 08 Aug 2020 13:21:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7217780/SRX7217780.20_model.r WARNING @ Sat, 08 Aug 2020 13:21:11: #2 Since the d (203) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:21:11: #2 You may need to consider one of the other alternative d(s): 203 WARNING @ Sat, 08 Aug 2020 13:21:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 13:21:11: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:21:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:21:20: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:21:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7217780/SRX7217780.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:21:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7217780/SRX7217780.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:21:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7217780/SRX7217780.20_summits.bed INFO @ Sat, 08 Aug 2020 13:21:24: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (157 records, 4 fields): 1 millis CompletedMACS2peakCalling