Job ID = 6367845 SRX = SRX4085413 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:37:44 prefetch.2.10.7: 1) Downloading 'SRR7167442'... 2020-06-15T23:37:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:44:18 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:44:18 prefetch.2.10.7: 1) 'SRR7167442' was downloaded successfully Read 18770721 spots for SRR7167442/SRR7167442.sra Written 18770721 spots for SRR7167442/SRR7167442.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: 00:00:01 Multiseed full-index search: 00:10:52 18770721 reads; of these: 18770721 (100.00%) were paired; of these: 10794034 (57.50%) aligned concordantly 0 times 6544291 (34.86%) aligned concordantly exactly 1 time 1432396 (7.63%) aligned concordantly >1 times ---- 10794034 pairs aligned concordantly 0 times; of these: 418711 (3.88%) aligned discordantly 1 time ---- 10375323 pairs aligned 0 times concordantly or discordantly; of these: 20750646 mates make up the pairs; of these: 14380040 (69.30%) aligned 0 times 5678708 (27.37%) aligned exactly 1 time 691898 (3.33%) aligned >1 times 61.70% overall alignment rate Time searching: 00:10:53 Overall time: 00:10:53 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] 1114554 / 8229289 = 0.1354 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 09:03:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085413/SRX4085413.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085413/SRX4085413.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085413/SRX4085413.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085413/SRX4085413.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 09:03:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:03:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:04:06: 1000000 INFO @ Tue, 16 Jun 2020 09:04:14: 2000000 INFO @ Tue, 16 Jun 2020 09:04:21: 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 @ Tue, 16 Jun 2020 09:04:29: 4000000 INFO @ Tue, 16 Jun 2020 09:04:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085413/SRX4085413.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085413/SRX4085413.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085413/SRX4085413.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085413/SRX4085413.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 09:04:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:04:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:04:37: 1000000 INFO @ Tue, 16 Jun 2020 09:04:37: 5000000 INFO @ Tue, 16 Jun 2020 09:04:45: 2000000 INFO @ Tue, 16 Jun 2020 09:04:45: 6000000 INFO @ Tue, 16 Jun 2020 09:04:53: 3000000 INFO @ Tue, 16 Jun 2020 09:04:54: 7000000 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 09:04:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085413/SRX4085413.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085413/SRX4085413.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085413/SRX4085413.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085413/SRX4085413.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 09:04:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:04:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:05:01: 4000000 INFO @ Tue, 16 Jun 2020 09:05:03: 8000000 INFO @ Tue, 16 Jun 2020 09:05:07: 1000000 INFO @ Tue, 16 Jun 2020 09:05:09: 5000000 INFO @ Tue, 16 Jun 2020 09:05:12: 9000000 INFO @ Tue, 16 Jun 2020 09:05:15: 2000000 INFO @ Tue, 16 Jun 2020 09:05:18: 6000000 INFO @ Tue, 16 Jun 2020 09:05:21: 10000000 INFO @ Tue, 16 Jun 2020 09:05:24: 3000000 INFO @ Tue, 16 Jun 2020 09:05:26: 7000000 INFO @ Tue, 16 Jun 2020 09:05:29: 11000000 INFO @ Tue, 16 Jun 2020 09:05:32: 4000000 INFO @ Tue, 16 Jun 2020 09:05:34: 8000000 INFO @ Tue, 16 Jun 2020 09:05:38: 12000000 INFO @ Tue, 16 Jun 2020 09:05:40: 5000000 INFO @ Tue, 16 Jun 2020 09:05:42: 9000000 INFO @ Tue, 16 Jun 2020 09:05:46: 13000000 INFO @ Tue, 16 Jun 2020 09:05:48: 6000000 INFO @ Tue, 16 Jun 2020 09:05:50: 10000000 INFO @ Tue, 16 Jun 2020 09:05:55: 14000000 INFO @ Tue, 16 Jun 2020 09:05:56: 7000000 INFO @ Tue, 16 Jun 2020 09:05:58: 11000000 INFO @ Tue, 16 Jun 2020 09:06:03: 15000000 INFO @ Tue, 16 Jun 2020 09:06:04: 8000000 INFO @ Tue, 16 Jun 2020 09:06:06: 12000000 INFO @ Tue, 16 Jun 2020 09:06:12: 16000000 INFO @ Tue, 16 Jun 2020 09:06:12: 9000000 INFO @ Tue, 16 Jun 2020 09:06:15: 13000000 INFO @ Tue, 16 Jun 2020 09:06:20: 17000000 INFO @ Tue, 16 Jun 2020 09:06:20: 10000000 INFO @ Tue, 16 Jun 2020 09:06:22: 14000000 INFO @ Tue, 16 Jun 2020 09:06:28: 11000000 INFO @ Tue, 16 Jun 2020 09:06:28: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:06:30: 15000000 INFO @ Tue, 16 Jun 2020 09:06:36: 12000000 INFO @ Tue, 16 Jun 2020 09:06:36: 19000000 INFO @ Tue, 16 Jun 2020 09:06:38: 16000000 INFO @ Tue, 16 Jun 2020 09:06:44: 13000000 INFO @ Tue, 16 Jun 2020 09:06:44: 20000000 INFO @ Tue, 16 Jun 2020 09:06:46: 17000000 INFO @ Tue, 16 Jun 2020 09:06:51: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:06:51: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:06:51: #1 total tags in treatment: 6894845 INFO @ Tue, 16 Jun 2020 09:06:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:06:51: #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 09:06:51: #1 tags after filtering in treatment: 5599577 INFO @ Tue, 16 Jun 2020 09:06:51: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 16 Jun 2020 09:06:51: #1 finished! INFO @ Tue, 16 Jun 2020 09:06:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:06:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:06:51: 14000000 INFO @ Tue, 16 Jun 2020 09:06:52: #2 number of paired peaks: 1241 INFO @ Tue, 16 Jun 2020 09:06:52: start model_add_line... INFO @ Tue, 16 Jun 2020 09:06:52: start X-correlation... INFO @ Tue, 16 Jun 2020 09:06:52: end of X-cor INFO @ Tue, 16 Jun 2020 09:06:52: #2 finished! INFO @ Tue, 16 Jun 2020 09:06:52: #2 predicted fragment length is 83 bps INFO @ Tue, 16 Jun 2020 09:06:52: #2 alternative fragment length(s) may be 83 bps INFO @ Tue, 16 Jun 2020 09:06:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085413/SRX4085413.05_model.r WARNING @ Tue, 16 Jun 2020 09:06:52: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:06:52: #2 You may need to consider one of the other alternative d(s): 83 WARNING @ Tue, 16 Jun 2020 09:06:52: #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 09:06:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:06:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:06:54: 18000000 INFO @ Tue, 16 Jun 2020 09:06:58: 15000000 INFO @ Tue, 16 Jun 2020 09:07:01: 19000000 INFO @ Tue, 16 Jun 2020 09:07:05: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:07:05: 16000000 INFO @ Tue, 16 Jun 2020 09:07:07: 20000000 INFO @ Tue, 16 Jun 2020 09:07:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085413/SRX4085413.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:07:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085413/SRX4085413.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:07:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085413/SRX4085413.05_summits.bed INFO @ Tue, 16 Jun 2020 09:07:12: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7554 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:07:12: 17000000 INFO @ Tue, 16 Jun 2020 09:07:13: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:07:13: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:07:13: #1 total tags in treatment: 6894845 INFO @ Tue, 16 Jun 2020 09:07:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:07:13: #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 09:07:13: #1 tags after filtering in treatment: 5599577 INFO @ Tue, 16 Jun 2020 09:07:13: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 16 Jun 2020 09:07:13: #1 finished! INFO @ Tue, 16 Jun 2020 09:07:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:07:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:07:14: #2 number of paired peaks: 1241 INFO @ Tue, 16 Jun 2020 09:07:14: start model_add_line... INFO @ Tue, 16 Jun 2020 09:07:14: start X-correlation... INFO @ Tue, 16 Jun 2020 09:07:14: end of X-cor INFO @ Tue, 16 Jun 2020 09:07:14: #2 finished! INFO @ Tue, 16 Jun 2020 09:07:14: #2 predicted fragment length is 83 bps INFO @ Tue, 16 Jun 2020 09:07:14: #2 alternative fragment length(s) may be 83 bps INFO @ Tue, 16 Jun 2020 09:07:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085413/SRX4085413.10_model.r WARNING @ Tue, 16 Jun 2020 09:07:14: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:07:14: #2 You may need to consider one of the other alternative d(s): 83 WARNING @ Tue, 16 Jun 2020 09:07:14: #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 09:07:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:07:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:07:19: 18000000 INFO @ Tue, 16 Jun 2020 09:07:25: 19000000 INFO @ Tue, 16 Jun 2020 09:07:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:07:30: 20000000 INFO @ Tue, 16 Jun 2020 09:07:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085413/SRX4085413.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:07:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085413/SRX4085413.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:07:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085413/SRX4085413.10_summits.bed INFO @ Tue, 16 Jun 2020 09:07:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4638 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:07:35: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:07:35: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:07:35: #1 total tags in treatment: 6894845 INFO @ Tue, 16 Jun 2020 09:07:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:07:35: #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 09:07:35: #1 tags after filtering in treatment: 5599577 INFO @ Tue, 16 Jun 2020 09:07:35: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 16 Jun 2020 09:07:35: #1 finished! INFO @ Tue, 16 Jun 2020 09:07:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:07:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:07:35: #2 number of paired peaks: 1241 INFO @ Tue, 16 Jun 2020 09:07:35: start model_add_line... INFO @ Tue, 16 Jun 2020 09:07:36: start X-correlation... INFO @ Tue, 16 Jun 2020 09:07:36: end of X-cor INFO @ Tue, 16 Jun 2020 09:07:36: #2 finished! INFO @ Tue, 16 Jun 2020 09:07:36: #2 predicted fragment length is 83 bps INFO @ Tue, 16 Jun 2020 09:07:36: #2 alternative fragment length(s) may be 83 bps INFO @ Tue, 16 Jun 2020 09:07:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085413/SRX4085413.20_model.r WARNING @ Tue, 16 Jun 2020 09:07:36: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:07:36: #2 You may need to consider one of the other alternative d(s): 83 WARNING @ Tue, 16 Jun 2020 09:07:36: #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 09:07:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:07:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:07:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:07:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085413/SRX4085413.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:07:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085413/SRX4085413.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:07:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085413/SRX4085413.20_summits.bed INFO @ Tue, 16 Jun 2020 09:07:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2431 records, 4 fields): 3 millis CompletedMACS2peakCalling