Job ID = 6367667 SRX = SRX3733161 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:34:20 prefetch.2.10.7: 1) Downloading 'SRR6760674'... 2020-06-15T23:34:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:46:54 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:46:54 prefetch.2.10.7: 1) 'SRR6760674' was downloaded successfully 2020-06-15T23:46:54 prefetch.2.10.7: 'SRR6760674' has 0 unresolved dependencies Read 29694149 spots for SRR6760674/SRR6760674.sra Written 29694149 spots for SRR6760674/SRR6760674.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: 00:37:08 29694149 reads; of these: 29694149 (100.00%) were paired; of these: 2003177 (6.75%) aligned concordantly 0 times 24808045 (83.55%) aligned concordantly exactly 1 time 2882927 (9.71%) aligned concordantly >1 times ---- 2003177 pairs aligned concordantly 0 times; of these: 557629 (27.84%) aligned discordantly 1 time ---- 1445548 pairs aligned 0 times concordantly or discordantly; of these: 2891096 mates make up the pairs; of these: 2092238 (72.37%) aligned 0 times 528677 (18.29%) aligned exactly 1 time 270181 (9.35%) aligned >1 times 96.48% overall alignment rate Time searching: 00:37:08 Overall time: 00:37:08 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 24 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] 14890814 / 28195887 = 0.5281 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 09:41:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3733161/SRX3733161.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3733161/SRX3733161.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3733161/SRX3733161.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3733161/SRX3733161.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 09:41:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:41:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:41:39: 1000000 INFO @ Tue, 16 Jun 2020 09:41:44: 2000000 INFO @ Tue, 16 Jun 2020 09:41:50: 3000000 INFO @ Tue, 16 Jun 2020 09:41:55: 4000000 INFO @ Tue, 16 Jun 2020 09:42:00: 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 09:42:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3733161/SRX3733161.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3733161/SRX3733161.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3733161/SRX3733161.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3733161/SRX3733161.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 09:42:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:42:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:42:06: 6000000 INFO @ Tue, 16 Jun 2020 09:42:10: 1000000 INFO @ Tue, 16 Jun 2020 09:42:11: 7000000 INFO @ Tue, 16 Jun 2020 09:42:16: 2000000 INFO @ Tue, 16 Jun 2020 09:42:16: 8000000 INFO @ Tue, 16 Jun 2020 09:42:22: 9000000 INFO @ Tue, 16 Jun 2020 09:42:23: 3000000 INFO @ Tue, 16 Jun 2020 09:42:27: 10000000 INFO @ Tue, 16 Jun 2020 09:42:29: 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 09:42:33: 11000000 INFO @ Tue, 16 Jun 2020 09:42:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3733161/SRX3733161.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3733161/SRX3733161.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3733161/SRX3733161.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3733161/SRX3733161.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 09:42:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:42:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:42:35: 5000000 INFO @ Tue, 16 Jun 2020 09:42:38: 12000000 INFO @ Tue, 16 Jun 2020 09:42:40: 1000000 INFO @ Tue, 16 Jun 2020 09:42:42: 6000000 INFO @ Tue, 16 Jun 2020 09:42:44: 13000000 INFO @ Tue, 16 Jun 2020 09:42:45: 2000000 INFO @ Tue, 16 Jun 2020 09:42:48: 7000000 INFO @ Tue, 16 Jun 2020 09:42:49: 14000000 INFO @ Tue, 16 Jun 2020 09:42:51: 3000000 INFO @ Tue, 16 Jun 2020 09:42:54: 8000000 INFO @ Tue, 16 Jun 2020 09:42:55: 15000000 INFO @ Tue, 16 Jun 2020 09:42:57: 4000000 INFO @ Tue, 16 Jun 2020 09:43:01: 16000000 INFO @ Tue, 16 Jun 2020 09:43:01: 9000000 INFO @ Tue, 16 Jun 2020 09:43:02: 5000000 INFO @ Tue, 16 Jun 2020 09:43:06: 17000000 INFO @ Tue, 16 Jun 2020 09:43:07: 10000000 INFO @ Tue, 16 Jun 2020 09:43:08: 6000000 INFO @ Tue, 16 Jun 2020 09:43:12: 18000000 INFO @ Tue, 16 Jun 2020 09:43:13: 11000000 INFO @ Tue, 16 Jun 2020 09:43:14: 7000000 INFO @ Tue, 16 Jun 2020 09:43:17: 19000000 INFO @ Tue, 16 Jun 2020 09:43:19: 8000000 INFO @ Tue, 16 Jun 2020 09:43:20: 12000000 INFO @ Tue, 16 Jun 2020 09:43:23: 20000000 INFO @ Tue, 16 Jun 2020 09:43:25: 9000000 INFO @ Tue, 16 Jun 2020 09:43:26: 13000000 INFO @ Tue, 16 Jun 2020 09:43:28: 21000000 INFO @ Tue, 16 Jun 2020 09:43:30: 10000000 INFO @ Tue, 16 Jun 2020 09:43:32: 14000000 INFO @ Tue, 16 Jun 2020 09:43:33: 22000000 INFO @ Tue, 16 Jun 2020 09:43:36: 11000000 INFO @ Tue, 16 Jun 2020 09:43:39: 15000000 INFO @ Tue, 16 Jun 2020 09:43:39: 23000000 INFO @ Tue, 16 Jun 2020 09:43:42: 12000000 INFO @ Tue, 16 Jun 2020 09:43:44: 24000000 INFO @ Tue, 16 Jun 2020 09:43:45: 16000000 INFO @ Tue, 16 Jun 2020 09:43:47: 13000000 INFO @ Tue, 16 Jun 2020 09:43:50: 25000000 INFO @ Tue, 16 Jun 2020 09:43:51: 17000000 INFO @ Tue, 16 Jun 2020 09:43:53: 14000000 INFO @ Tue, 16 Jun 2020 09:43:55: 26000000 INFO @ Tue, 16 Jun 2020 09:43:57: 18000000 INFO @ Tue, 16 Jun 2020 09:43:58: 15000000 INFO @ Tue, 16 Jun 2020 09:44:01: 27000000 INFO @ Tue, 16 Jun 2020 09:44:03: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:44:03: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:44:03: #1 total tags in treatment: 12962198 INFO @ Tue, 16 Jun 2020 09:44:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:44:03: #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 09:44:04: #1 tags after filtering in treatment: 11029369 INFO @ Tue, 16 Jun 2020 09:44:04: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 16 Jun 2020 09:44:04: #1 finished! INFO @ Tue, 16 Jun 2020 09:44:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:44:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:44:04: 16000000 INFO @ Tue, 16 Jun 2020 09:44:04: 19000000 INFO @ Tue, 16 Jun 2020 09:44:04: #2 number of paired peaks: 456 WARNING @ Tue, 16 Jun 2020 09:44:04: Fewer paired peaks (456) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 456 pairs to build model! INFO @ Tue, 16 Jun 2020 09:44:04: start model_add_line... INFO @ Tue, 16 Jun 2020 09:44:04: start X-correlation... INFO @ Tue, 16 Jun 2020 09:44:04: end of X-cor INFO @ Tue, 16 Jun 2020 09:44:04: #2 finished! INFO @ Tue, 16 Jun 2020 09:44:04: #2 predicted fragment length is 144 bps INFO @ Tue, 16 Jun 2020 09:44:04: #2 alternative fragment length(s) may be 4,128,144 bps INFO @ Tue, 16 Jun 2020 09:44:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3733161/SRX3733161.05_model.r WARNING @ Tue, 16 Jun 2020 09:44:04: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:44:04: #2 You may need to consider one of the other alternative d(s): 4,128,144 WARNING @ Tue, 16 Jun 2020 09:44:04: #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 09:44:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:44:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:44:09: 17000000 INFO @ Tue, 16 Jun 2020 09:44:10: 20000000 INFO @ Tue, 16 Jun 2020 09:44:14: 18000000 INFO @ Tue, 16 Jun 2020 09:44:16: 21000000 INFO @ Tue, 16 Jun 2020 09:44:20: 19000000 INFO @ Tue, 16 Jun 2020 09:44:22: 22000000 INFO @ Tue, 16 Jun 2020 09:44:25: 20000000 INFO @ Tue, 16 Jun 2020 09:44:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:44:28: 23000000 INFO @ Tue, 16 Jun 2020 09:44:30: 21000000 INFO @ Tue, 16 Jun 2020 09:44:34: 24000000 INFO @ Tue, 16 Jun 2020 09:44:35: 22000000 INFO @ Tue, 16 Jun 2020 09:44:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3733161/SRX3733161.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:44:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3733161/SRX3733161.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:44:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3733161/SRX3733161.05_summits.bed INFO @ Tue, 16 Jun 2020 09:44:38: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (508 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:44:40: 25000000 INFO @ Tue, 16 Jun 2020 09:44:41: 23000000 INFO @ Tue, 16 Jun 2020 09:44:46: 24000000 INFO @ Tue, 16 Jun 2020 09:44:46: 26000000 INFO @ Tue, 16 Jun 2020 09:44:51: 25000000 INFO @ Tue, 16 Jun 2020 09:44:52: 27000000 INFO @ Tue, 16 Jun 2020 09:44:56: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:44:56: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:44:56: #1 total tags in treatment: 12962198 INFO @ Tue, 16 Jun 2020 09:44:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:44:56: #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 09:44:56: #1 tags after filtering in treatment: 11029369 INFO @ Tue, 16 Jun 2020 09:44:56: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 16 Jun 2020 09:44:56: #1 finished! INFO @ Tue, 16 Jun 2020 09:44:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:44:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:44:57: 26000000 INFO @ Tue, 16 Jun 2020 09:44:57: #2 number of paired peaks: 456 WARNING @ Tue, 16 Jun 2020 09:44:57: Fewer paired peaks (456) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 456 pairs to build model! INFO @ Tue, 16 Jun 2020 09:44:57: start model_add_line... INFO @ Tue, 16 Jun 2020 09:44:57: start X-correlation... INFO @ Tue, 16 Jun 2020 09:44:57: end of X-cor INFO @ Tue, 16 Jun 2020 09:44:57: #2 finished! INFO @ Tue, 16 Jun 2020 09:44:57: #2 predicted fragment length is 144 bps INFO @ Tue, 16 Jun 2020 09:44:57: #2 alternative fragment length(s) may be 4,128,144 bps INFO @ Tue, 16 Jun 2020 09:44:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3733161/SRX3733161.10_model.r WARNING @ Tue, 16 Jun 2020 09:44:57: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:44:57: #2 You may need to consider one of the other alternative d(s): 4,128,144 WARNING @ Tue, 16 Jun 2020 09:44:57: #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 09:44:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:44:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:45:02: 27000000 INFO @ Tue, 16 Jun 2020 09:45:05: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:45:05: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:45:05: #1 total tags in treatment: 12962198 INFO @ Tue, 16 Jun 2020 09:45:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:45:05: #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 09:45:05: #1 tags after filtering in treatment: 11029369 INFO @ Tue, 16 Jun 2020 09:45:05: #1 Redundant rate of treatment: 0.15 INFO @ Tue, 16 Jun 2020 09:45:05: #1 finished! INFO @ Tue, 16 Jun 2020 09:45:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:45:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:45:06: #2 number of paired peaks: 456 WARNING @ Tue, 16 Jun 2020 09:45:06: Fewer paired peaks (456) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 456 pairs to build model! INFO @ Tue, 16 Jun 2020 09:45:06: start model_add_line... INFO @ Tue, 16 Jun 2020 09:45:06: start X-correlation... INFO @ Tue, 16 Jun 2020 09:45:06: end of X-cor INFO @ Tue, 16 Jun 2020 09:45:06: #2 finished! INFO @ Tue, 16 Jun 2020 09:45:06: #2 predicted fragment length is 144 bps INFO @ Tue, 16 Jun 2020 09:45:06: #2 alternative fragment length(s) may be 4,128,144 bps INFO @ Tue, 16 Jun 2020 09:45:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3733161/SRX3733161.20_model.r WARNING @ Tue, 16 Jun 2020 09:45:06: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:45:06: #2 You may need to consider one of the other alternative d(s): 4,128,144 WARNING @ Tue, 16 Jun 2020 09:45:06: #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 09:45:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:45:06: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:45:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:45:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:45:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3733161/SRX3733161.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:45:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3733161/SRX3733161.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:45:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3733161/SRX3733161.10_summits.bed INFO @ Tue, 16 Jun 2020 09:45:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (355 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:45:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3733161/SRX3733161.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:45:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3733161/SRX3733161.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:45:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3733161/SRX3733161.20_summits.bed INFO @ Tue, 16 Jun 2020 09:45:39: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (232 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。