Job ID = 6368954 SRX = SRX7627594 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:36:04 prefetch.2.10.7: 1) Downloading 'SRR10961944'... 2020-06-16T00:36:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:39:47 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:39:47 prefetch.2.10.7: 1) 'SRR10961944' was downloaded successfully Read 29918182 spots for SRR10961944/SRR10961944.sra Written 29918182 spots for SRR10961944/SRR10961944.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: 00:04:28 29918182 reads; of these: 29918182 (100.00%) were unpaired; of these: 15694753 (52.46%) aligned 0 times 11775006 (39.36%) aligned exactly 1 time 2448423 (8.18%) aligned >1 times 47.54% overall alignment rate Time searching: 00:04:28 Overall time: 00:04:28 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] 2113352 / 14223429 = 0.1486 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 09:49:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7627594/SRX7627594.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7627594/SRX7627594.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7627594/SRX7627594.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7627594/SRX7627594.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 09:49:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:49:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:49:32: 1000000 INFO @ Tue, 16 Jun 2020 09:49:38: 2000000 INFO @ Tue, 16 Jun 2020 09:49:44: 3000000 INFO @ Tue, 16 Jun 2020 09:49:50: 4000000 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 09:49:55: 5000000 INFO @ Tue, 16 Jun 2020 09:49:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7627594/SRX7627594.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7627594/SRX7627594.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7627594/SRX7627594.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7627594/SRX7627594.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 09:49:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:49:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:50:02: 6000000 INFO @ Tue, 16 Jun 2020 09:50:03: 1000000 INFO @ Tue, 16 Jun 2020 09:50:08: 7000000 INFO @ Tue, 16 Jun 2020 09:50:10: 2000000 INFO @ Tue, 16 Jun 2020 09:50:15: 8000000 INFO @ Tue, 16 Jun 2020 09:50:16: 3000000 INFO @ Tue, 16 Jun 2020 09:50:21: 9000000 INFO @ Tue, 16 Jun 2020 09:50:23: 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 09:50:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7627594/SRX7627594.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7627594/SRX7627594.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7627594/SRX7627594.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7627594/SRX7627594.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 09:50:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:50:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:50:28: 10000000 INFO @ Tue, 16 Jun 2020 09:50:29: 5000000 INFO @ Tue, 16 Jun 2020 09:50:33: 1000000 INFO @ Tue, 16 Jun 2020 09:50:34: 11000000 INFO @ Tue, 16 Jun 2020 09:50:36: 6000000 INFO @ Tue, 16 Jun 2020 09:50:40: 2000000 INFO @ Tue, 16 Jun 2020 09:50:41: 12000000 INFO @ Tue, 16 Jun 2020 09:50:42: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:50:42: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:50:42: #1 total tags in treatment: 12110077 INFO @ Tue, 16 Jun 2020 09:50:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:50:42: #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 09:50:42: #1 tags after filtering in treatment: 12110077 INFO @ Tue, 16 Jun 2020 09:50:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:50:42: #1 finished! INFO @ Tue, 16 Jun 2020 09:50:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:50:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:50:43: 7000000 INFO @ Tue, 16 Jun 2020 09:50:43: #2 number of paired peaks: 353 WARNING @ Tue, 16 Jun 2020 09:50:43: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Tue, 16 Jun 2020 09:50:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:50:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:50:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:50:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:50:43: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:50:43: #2 alternative fragment length(s) may be 3,49 bps INFO @ Tue, 16 Jun 2020 09:50:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7627594/SRX7627594.05_model.r WARNING @ Tue, 16 Jun 2020 09:50:43: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:50:43: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Tue, 16 Jun 2020 09:50:43: #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 09:50:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:50:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:50:47: 3000000 INFO @ Tue, 16 Jun 2020 09:50:49: 8000000 INFO @ Tue, 16 Jun 2020 09:50:54: 4000000 INFO @ Tue, 16 Jun 2020 09:50:56: 9000000 INFO @ Tue, 16 Jun 2020 09:51:01: 5000000 INFO @ Tue, 16 Jun 2020 09:51:03: 10000000 INFO @ Tue, 16 Jun 2020 09:51:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:51:07: 6000000 INFO @ Tue, 16 Jun 2020 09:51:10: 11000000 INFO @ Tue, 16 Jun 2020 09:51:14: 7000000 INFO @ Tue, 16 Jun 2020 09:51:17: 12000000 INFO @ Tue, 16 Jun 2020 09:51:17: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:51:17: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:51:17: #1 total tags in treatment: 12110077 INFO @ Tue, 16 Jun 2020 09:51:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:51:17: #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 09:51:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7627594/SRX7627594.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:51:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7627594/SRX7627594.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:51:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7627594/SRX7627594.05_summits.bed INFO @ Tue, 16 Jun 2020 09:51:17: Done! INFO @ Tue, 16 Jun 2020 09:51:17: #1 tags after filtering in treatment: 12110077 INFO @ Tue, 16 Jun 2020 09:51:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:51:17: #1 finished! INFO @ Tue, 16 Jun 2020 09:51:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:51:17: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (915 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:51:18: #2 number of paired peaks: 353 WARNING @ Tue, 16 Jun 2020 09:51:18: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Tue, 16 Jun 2020 09:51:18: start model_add_line... INFO @ Tue, 16 Jun 2020 09:51:18: start X-correlation... INFO @ Tue, 16 Jun 2020 09:51:18: end of X-cor INFO @ Tue, 16 Jun 2020 09:51:18: #2 finished! INFO @ Tue, 16 Jun 2020 09:51:18: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:51:18: #2 alternative fragment length(s) may be 3,49 bps INFO @ Tue, 16 Jun 2020 09:51:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7627594/SRX7627594.10_model.r WARNING @ Tue, 16 Jun 2020 09:51:18: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:51:18: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Tue, 16 Jun 2020 09:51:18: #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 09:51:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:51:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:51:21: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:51:27: 9000000 INFO @ Tue, 16 Jun 2020 09:51:33: 10000000 INFO @ Tue, 16 Jun 2020 09:51:39: 11000000 INFO @ Tue, 16 Jun 2020 09:51:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:51:45: 12000000 INFO @ Tue, 16 Jun 2020 09:51:45: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:51:45: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:51:45: #1 total tags in treatment: 12110077 INFO @ Tue, 16 Jun 2020 09:51:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:51:45: #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 09:51:45: #1 tags after filtering in treatment: 12110077 INFO @ Tue, 16 Jun 2020 09:51:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:51:45: #1 finished! INFO @ Tue, 16 Jun 2020 09:51:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:51:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:51:46: #2 number of paired peaks: 353 WARNING @ Tue, 16 Jun 2020 09:51:46: Fewer paired peaks (353) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 353 pairs to build model! INFO @ Tue, 16 Jun 2020 09:51:46: start model_add_line... INFO @ Tue, 16 Jun 2020 09:51:46: start X-correlation... INFO @ Tue, 16 Jun 2020 09:51:46: end of X-cor INFO @ Tue, 16 Jun 2020 09:51:46: #2 finished! INFO @ Tue, 16 Jun 2020 09:51:46: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:51:46: #2 alternative fragment length(s) may be 3,49 bps INFO @ Tue, 16 Jun 2020 09:51:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7627594/SRX7627594.20_model.r WARNING @ Tue, 16 Jun 2020 09:51:46: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:51:46: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Tue, 16 Jun 2020 09:51:46: #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 09:51:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:51:46: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:51:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7627594/SRX7627594.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:51:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7627594/SRX7627594.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:51:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7627594/SRX7627594.10_summits.bed INFO @ Tue, 16 Jun 2020 09:51:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (527 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:52:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:52:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7627594/SRX7627594.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:52:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7627594/SRX7627594.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:52:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7627594/SRX7627594.20_summits.bed INFO @ Tue, 16 Jun 2020 09:52:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (216 records, 4 fields): 1 millis CompletedMACS2peakCalling