Job ID = 6497496 SRX = SRX495017 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:47:28 prefetch.2.10.7: 1) Downloading 'SRR1198549'... 2020-06-25T22:47:28 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:49:00 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:49:01 prefetch.2.10.7: 'SRR1198549' is valid 2020-06-25T22:49:01 prefetch.2.10.7: 1) 'SRR1198549' was downloaded successfully Read 13338445 spots for SRR1198549/SRR1198549.sra Written 13338445 spots for SRR1198549/SRR1198549.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: 00:02:33 13338445 reads; of these: 13338445 (100.00%) were unpaired; of these: 89010 (0.67%) aligned 0 times 10992277 (82.41%) aligned exactly 1 time 2257158 (16.92%) aligned >1 times 99.33% overall alignment rate Time searching: 00:02:33 Overall time: 00:02:33 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_rmdupse_core] 2113818 / 13249435 = 0.1595 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 @ Fri, 26 Jun 2020 07:55:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495017/SRX495017.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495017/SRX495017.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495017/SRX495017.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495017/SRX495017.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 @ Fri, 26 Jun 2020 07:55:23: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:55:23: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:55:28: 1000000 INFO @ Fri, 26 Jun 2020 07:55:34: 2000000 INFO @ Fri, 26 Jun 2020 07:55:40: 3000000 INFO @ Fri, 26 Jun 2020 07:55:45: 4000000 INFO @ Fri, 26 Jun 2020 07:55:51: 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 @ Fri, 26 Jun 2020 07:55:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495017/SRX495017.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495017/SRX495017.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495017/SRX495017.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495017/SRX495017.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 @ Fri, 26 Jun 2020 07:55:53: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:55:53: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:55:57: 6000000 INFO @ Fri, 26 Jun 2020 07:56:00: 1000000 INFO @ Fri, 26 Jun 2020 07:56:04: 7000000 INFO @ Fri, 26 Jun 2020 07:56:06: 2000000 INFO @ Fri, 26 Jun 2020 07:56:10: 8000000 INFO @ Fri, 26 Jun 2020 07:56:13: 3000000 INFO @ Fri, 26 Jun 2020 07:56:17: 9000000 INFO @ Fri, 26 Jun 2020 07:56:19: 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 @ Fri, 26 Jun 2020 07:56:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495017/SRX495017.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495017/SRX495017.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495017/SRX495017.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495017/SRX495017.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 @ Fri, 26 Jun 2020 07:56:23: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:56:23: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:56:23: 10000000 INFO @ Fri, 26 Jun 2020 07:56:26: 5000000 INFO @ Fri, 26 Jun 2020 07:56:30: 11000000 INFO @ Fri, 26 Jun 2020 07:56:30: 1000000 INFO @ Fri, 26 Jun 2020 07:56:31: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 07:56:31: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 07:56:31: #1 total tags in treatment: 11135617 INFO @ Fri, 26 Jun 2020 07:56:31: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:56:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:56:31: #1 tags after filtering in treatment: 11135617 INFO @ Fri, 26 Jun 2020 07:56:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:56:31: #1 finished! INFO @ Fri, 26 Jun 2020 07:56:31: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:56:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:56:32: #2 number of paired peaks: 363 WARNING @ Fri, 26 Jun 2020 07:56:32: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Fri, 26 Jun 2020 07:56:32: start model_add_line... INFO @ Fri, 26 Jun 2020 07:56:32: start X-correlation... INFO @ Fri, 26 Jun 2020 07:56:32: end of X-cor INFO @ Fri, 26 Jun 2020 07:56:32: #2 finished! INFO @ Fri, 26 Jun 2020 07:56:32: #2 predicted fragment length is 41 bps INFO @ Fri, 26 Jun 2020 07:56:32: #2 alternative fragment length(s) may be 2,41 bps INFO @ Fri, 26 Jun 2020 07:56:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495017/SRX495017.05_model.r WARNING @ Fri, 26 Jun 2020 07:56:32: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:56:32: #2 You may need to consider one of the other alternative d(s): 2,41 WARNING @ Fri, 26 Jun 2020 07:56:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:56:32: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:56:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:56:32: 6000000 INFO @ Fri, 26 Jun 2020 07:56:37: 2000000 INFO @ Fri, 26 Jun 2020 07:56:39: 7000000 INFO @ Fri, 26 Jun 2020 07:56:44: 3000000 INFO @ Fri, 26 Jun 2020 07:56:46: 8000000 INFO @ Fri, 26 Jun 2020 07:56:52: 4000000 INFO @ Fri, 26 Jun 2020 07:56:53: 9000000 INFO @ Fri, 26 Jun 2020 07:56:54: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:56:59: 5000000 INFO @ Fri, 26 Jun 2020 07:56:59: 10000000 INFO @ Fri, 26 Jun 2020 07:57:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495017/SRX495017.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:57:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495017/SRX495017.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:57:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495017/SRX495017.05_summits.bed INFO @ Fri, 26 Jun 2020 07:57:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (943 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:57:06: 6000000 INFO @ Fri, 26 Jun 2020 07:57:06: 11000000 INFO @ Fri, 26 Jun 2020 07:57:07: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 07:57:07: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 07:57:07: #1 total tags in treatment: 11135617 INFO @ Fri, 26 Jun 2020 07:57:07: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:57:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:57:07: #1 tags after filtering in treatment: 11135617 INFO @ Fri, 26 Jun 2020 07:57:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:57:07: #1 finished! INFO @ Fri, 26 Jun 2020 07:57:07: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:57:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:57:08: #2 number of paired peaks: 363 WARNING @ Fri, 26 Jun 2020 07:57:08: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Fri, 26 Jun 2020 07:57:08: start model_add_line... INFO @ Fri, 26 Jun 2020 07:57:08: start X-correlation... INFO @ Fri, 26 Jun 2020 07:57:08: end of X-cor INFO @ Fri, 26 Jun 2020 07:57:08: #2 finished! INFO @ Fri, 26 Jun 2020 07:57:08: #2 predicted fragment length is 41 bps INFO @ Fri, 26 Jun 2020 07:57:08: #2 alternative fragment length(s) may be 2,41 bps INFO @ Fri, 26 Jun 2020 07:57:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495017/SRX495017.10_model.r WARNING @ Fri, 26 Jun 2020 07:57:08: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:57:08: #2 You may need to consider one of the other alternative d(s): 2,41 WARNING @ Fri, 26 Jun 2020 07:57:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:57:08: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:57:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:57:12: 7000000 INFO @ Fri, 26 Jun 2020 07:57:19: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:57:25: 9000000 INFO @ Fri, 26 Jun 2020 07:57:31: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:57:32: 10000000 INFO @ Fri, 26 Jun 2020 07:57:38: 11000000 INFO @ Fri, 26 Jun 2020 07:57:39: #1 tag size is determined as 42 bps INFO @ Fri, 26 Jun 2020 07:57:39: #1 tag size = 42 INFO @ Fri, 26 Jun 2020 07:57:39: #1 total tags in treatment: 11135617 INFO @ Fri, 26 Jun 2020 07:57:39: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:57:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:57:40: #1 tags after filtering in treatment: 11135617 INFO @ Fri, 26 Jun 2020 07:57:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:57:40: #1 finished! INFO @ Fri, 26 Jun 2020 07:57:40: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:57:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:57:40: #2 number of paired peaks: 363 WARNING @ Fri, 26 Jun 2020 07:57:40: Fewer paired peaks (363) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 363 pairs to build model! INFO @ Fri, 26 Jun 2020 07:57:40: start model_add_line... INFO @ Fri, 26 Jun 2020 07:57:40: start X-correlation... INFO @ Fri, 26 Jun 2020 07:57:40: end of X-cor INFO @ Fri, 26 Jun 2020 07:57:40: #2 finished! INFO @ Fri, 26 Jun 2020 07:57:40: #2 predicted fragment length is 41 bps INFO @ Fri, 26 Jun 2020 07:57:40: #2 alternative fragment length(s) may be 2,41 bps INFO @ Fri, 26 Jun 2020 07:57:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495017/SRX495017.20_model.r WARNING @ Fri, 26 Jun 2020 07:57:40: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:57:40: #2 You may need to consider one of the other alternative d(s): 2,41 WARNING @ Fri, 26 Jun 2020 07:57:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:57:40: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:57:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:57:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495017/SRX495017.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:57:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495017/SRX495017.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:57:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495017/SRX495017.10_summits.bed INFO @ Fri, 26 Jun 2020 07:57:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (368 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:58:03: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:58:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495017/SRX495017.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:58:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495017/SRX495017.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:58:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495017/SRX495017.20_summits.bed INFO @ Fri, 26 Jun 2020 07:58:14: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (130 records, 4 fields): 2 millis CompletedMACS2peakCalling