Job ID = 6366275 SRX = SRX105309 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:43:37 prefetch.2.10.7: 1) Downloading 'SRR363996'... 2020-06-15T22:43:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:45:30 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:45:30 prefetch.2.10.7: 1) 'SRR363996' was downloaded successfully Read 20026814 spots for SRR363996/SRR363996.sra Written 20026814 spots for SRR363996/SRR363996.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: 00:03:42 20026814 reads; of these: 20026814 (100.00%) were unpaired; of these: 254456 (1.27%) aligned 0 times 16503796 (82.41%) aligned exactly 1 time 3268562 (16.32%) aligned >1 times 98.73% overall alignment rate Time searching: 00:03:42 Overall time: 00:03:42 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] 2190700 / 19772358 = 0.1108 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 07:55:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX105309/SRX105309.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX105309/SRX105309.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX105309/SRX105309.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX105309/SRX105309.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 07:55:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:55:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:55:13: 1000000 INFO @ Tue, 16 Jun 2020 07:55:19: 2000000 INFO @ Tue, 16 Jun 2020 07:55:26: 3000000 INFO @ Tue, 16 Jun 2020 07:55:32: 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 07:55:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX105309/SRX105309.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX105309/SRX105309.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX105309/SRX105309.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX105309/SRX105309.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 07:55:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:55:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:55:39: 5000000 INFO @ Tue, 16 Jun 2020 07:55:43: 1000000 INFO @ Tue, 16 Jun 2020 07:55:46: 6000000 INFO @ Tue, 16 Jun 2020 07:55:50: 2000000 INFO @ Tue, 16 Jun 2020 07:55:53: 7000000 INFO @ Tue, 16 Jun 2020 07:55:56: 3000000 INFO @ Tue, 16 Jun 2020 07:56:00: 8000000 INFO @ Tue, 16 Jun 2020 07:56:03: 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 07:56:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX105309/SRX105309.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX105309/SRX105309.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX105309/SRX105309.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX105309/SRX105309.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 07:56:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:56:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:56:07: 9000000 INFO @ Tue, 16 Jun 2020 07:56:09: 5000000 INFO @ Tue, 16 Jun 2020 07:56:14: 1000000 INFO @ Tue, 16 Jun 2020 07:56:15: 10000000 INFO @ Tue, 16 Jun 2020 07:56:16: 6000000 INFO @ Tue, 16 Jun 2020 07:56:21: 2000000 INFO @ Tue, 16 Jun 2020 07:56:22: 11000000 INFO @ Tue, 16 Jun 2020 07:56:23: 7000000 INFO @ Tue, 16 Jun 2020 07:56:29: 3000000 INFO @ Tue, 16 Jun 2020 07:56:29: 8000000 INFO @ Tue, 16 Jun 2020 07:56:30: 12000000 INFO @ Tue, 16 Jun 2020 07:56:36: 9000000 INFO @ Tue, 16 Jun 2020 07:56:37: 4000000 INFO @ Tue, 16 Jun 2020 07:56:37: 13000000 INFO @ Tue, 16 Jun 2020 07:56:43: 10000000 INFO @ Tue, 16 Jun 2020 07:56:44: 5000000 INFO @ Tue, 16 Jun 2020 07:56:44: 14000000 INFO @ Tue, 16 Jun 2020 07:56:50: 11000000 INFO @ Tue, 16 Jun 2020 07:56:52: 6000000 INFO @ Tue, 16 Jun 2020 07:56:52: 15000000 INFO @ Tue, 16 Jun 2020 07:56:56: 12000000 INFO @ Tue, 16 Jun 2020 07:56:59: 16000000 INFO @ Tue, 16 Jun 2020 07:56:59: 7000000 INFO @ Tue, 16 Jun 2020 07:57:03: 13000000 INFO @ Tue, 16 Jun 2020 07:57:07: 17000000 INFO @ Tue, 16 Jun 2020 07:57:07: 8000000 INFO @ Tue, 16 Jun 2020 07:57:10: 14000000 INFO @ Tue, 16 Jun 2020 07:57:11: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:57:11: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:57:11: #1 total tags in treatment: 17581658 INFO @ Tue, 16 Jun 2020 07:57:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:57:11: #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 07:57:12: #1 tags after filtering in treatment: 17581658 INFO @ Tue, 16 Jun 2020 07:57:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:57:12: #1 finished! INFO @ Tue, 16 Jun 2020 07:57:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:57:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:57:13: #2 number of paired peaks: 150 WARNING @ Tue, 16 Jun 2020 07:57:13: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Tue, 16 Jun 2020 07:57:13: start model_add_line... INFO @ Tue, 16 Jun 2020 07:57:13: start X-correlation... INFO @ Tue, 16 Jun 2020 07:57:13: end of X-cor INFO @ Tue, 16 Jun 2020 07:57:13: #2 finished! INFO @ Tue, 16 Jun 2020 07:57:13: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 07:57:13: #2 alternative fragment length(s) may be 1,34,543 bps INFO @ Tue, 16 Jun 2020 07:57:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX105309/SRX105309.05_model.r WARNING @ Tue, 16 Jun 2020 07:57:13: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:57:13: #2 You may need to consider one of the other alternative d(s): 1,34,543 WARNING @ Tue, 16 Jun 2020 07:57:13: #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 07:57:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:57:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:57:15: 9000000 INFO @ Tue, 16 Jun 2020 07:57:17: 15000000 INFO @ Tue, 16 Jun 2020 07:57:23: 10000000 INFO @ Tue, 16 Jun 2020 07:57:24: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:57:30: 17000000 INFO @ Tue, 16 Jun 2020 07:57:30: 11000000 INFO @ Tue, 16 Jun 2020 07:57:34: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:57:34: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:57:34: #1 total tags in treatment: 17581658 INFO @ Tue, 16 Jun 2020 07:57:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:57:34: #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 07:57:34: #1 tags after filtering in treatment: 17581658 INFO @ Tue, 16 Jun 2020 07:57:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:57:34: #1 finished! INFO @ Tue, 16 Jun 2020 07:57:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:57:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:57:36: #2 number of paired peaks: 150 WARNING @ Tue, 16 Jun 2020 07:57:36: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Tue, 16 Jun 2020 07:57:36: start model_add_line... INFO @ Tue, 16 Jun 2020 07:57:36: start X-correlation... INFO @ Tue, 16 Jun 2020 07:57:36: end of X-cor INFO @ Tue, 16 Jun 2020 07:57:36: #2 finished! INFO @ Tue, 16 Jun 2020 07:57:36: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 07:57:36: #2 alternative fragment length(s) may be 1,34,543 bps INFO @ Tue, 16 Jun 2020 07:57:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX105309/SRX105309.10_model.r WARNING @ Tue, 16 Jun 2020 07:57:36: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:57:36: #2 You may need to consider one of the other alternative d(s): 1,34,543 WARNING @ Tue, 16 Jun 2020 07:57:36: #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 07:57:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:57:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:57:38: 12000000 INFO @ Tue, 16 Jun 2020 07:57:45: 13000000 INFO @ Tue, 16 Jun 2020 07:57:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:57:52: 14000000 INFO @ Tue, 16 Jun 2020 07:57:59: 15000000 INFO @ Tue, 16 Jun 2020 07:58:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX105309/SRX105309.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:58:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX105309/SRX105309.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:58:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX105309/SRX105309.05_summits.bed INFO @ Tue, 16 Jun 2020 07:58:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (541 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:58:06: 16000000 INFO @ Tue, 16 Jun 2020 07:58:08: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:58:13: 17000000 INFO @ Tue, 16 Jun 2020 07:58:18: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:58:18: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:58:18: #1 total tags in treatment: 17581658 INFO @ Tue, 16 Jun 2020 07:58:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:58:18: #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 07:58:18: #1 tags after filtering in treatment: 17581658 INFO @ Tue, 16 Jun 2020 07:58:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:58:18: #1 finished! INFO @ Tue, 16 Jun 2020 07:58:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:58:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:58:19: #2 number of paired peaks: 150 WARNING @ Tue, 16 Jun 2020 07:58:19: Fewer paired peaks (150) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 150 pairs to build model! INFO @ Tue, 16 Jun 2020 07:58:19: start model_add_line... INFO @ Tue, 16 Jun 2020 07:58:19: start X-correlation... INFO @ Tue, 16 Jun 2020 07:58:19: end of X-cor INFO @ Tue, 16 Jun 2020 07:58:19: #2 finished! INFO @ Tue, 16 Jun 2020 07:58:19: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 07:58:19: #2 alternative fragment length(s) may be 1,34,543 bps INFO @ Tue, 16 Jun 2020 07:58:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX105309/SRX105309.20_model.r WARNING @ Tue, 16 Jun 2020 07:58:19: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:58:19: #2 You may need to consider one of the other alternative d(s): 1,34,543 WARNING @ Tue, 16 Jun 2020 07:58:19: #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 07:58:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:58:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:58:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX105309/SRX105309.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:58:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX105309/SRX105309.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:58:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX105309/SRX105309.10_summits.bed INFO @ Tue, 16 Jun 2020 07:58:24: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (236 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:58:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:59:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX105309/SRX105309.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:59:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX105309/SRX105309.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:59:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX105309/SRX105309.20_summits.bed INFO @ Tue, 16 Jun 2020 07:59:11: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (46 records, 4 fields): 1 millis CompletedMACS2peakCalling