Job ID = 6497460 SRX = SRX494961 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T21:20:14 prefetch.2.10.7: 1) Downloading 'SRR1198493'... 2020-06-25T21:20:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:23:33 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:23:33 prefetch.2.10.7: 1) 'SRR1198493' was downloaded successfully Read 36876981 spots for SRR1198493/SRR1198493.sra Written 36876981 spots for SRR1198493/SRR1198493.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: 00:06:41 36876981 reads; of these: 36876981 (100.00%) were unpaired; of these: 2081410 (5.64%) aligned 0 times 27052140 (73.36%) aligned exactly 1 time 7743431 (21.00%) aligned >1 times 94.36% overall alignment rate Time searching: 00:06:41 Overall time: 00:06:41 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_rmdupse_core] 25374711 / 34795571 = 0.7293 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 06:37:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494961/SRX494961.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494961/SRX494961.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494961/SRX494961.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494961/SRX494961.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 06:37:30: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:37:30: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:37:35: 1000000 INFO @ Fri, 26 Jun 2020 06:37:40: 2000000 INFO @ Fri, 26 Jun 2020 06:37:45: 3000000 INFO @ Fri, 26 Jun 2020 06:37:49: 4000000 INFO @ Fri, 26 Jun 2020 06:37:54: 5000000 INFO @ Fri, 26 Jun 2020 06:37:59: 6000000 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 06:38:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494961/SRX494961.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494961/SRX494961.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494961/SRX494961.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494961/SRX494961.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 06:38:01: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:38:01: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:38:04: 7000000 INFO @ Fri, 26 Jun 2020 06:38:06: 1000000 INFO @ Fri, 26 Jun 2020 06:38:09: 8000000 INFO @ Fri, 26 Jun 2020 06:38:11: 2000000 INFO @ Fri, 26 Jun 2020 06:38:14: 9000000 INFO @ Fri, 26 Jun 2020 06:38:16: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 06:38:16: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 06:38:16: #1 total tags in treatment: 9420860 INFO @ Fri, 26 Jun 2020 06:38:16: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:38:16: #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 06:38:16: 3000000 INFO @ Fri, 26 Jun 2020 06:38:16: #1 tags after filtering in treatment: 9420860 INFO @ Fri, 26 Jun 2020 06:38:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:38:16: #1 finished! INFO @ Fri, 26 Jun 2020 06:38:16: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:38:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:38:17: #2 number of paired peaks: 1660 INFO @ Fri, 26 Jun 2020 06:38:17: start model_add_line... INFO @ Fri, 26 Jun 2020 06:38:17: start X-correlation... INFO @ Fri, 26 Jun 2020 06:38:17: end of X-cor INFO @ Fri, 26 Jun 2020 06:38:17: #2 finished! INFO @ Fri, 26 Jun 2020 06:38:17: #2 predicted fragment length is 40 bps INFO @ Fri, 26 Jun 2020 06:38:17: #2 alternative fragment length(s) may be 3,40 bps INFO @ Fri, 26 Jun 2020 06:38:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494961/SRX494961.05_model.r INFO @ Fri, 26 Jun 2020 06:38:21: 4000000 WARNING @ Fri, 26 Jun 2020 06:38:21: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 06:38:21: #2 You may need to consider one of the other alternative d(s): 3,40 WARNING @ Fri, 26 Jun 2020 06:38:21: #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 06:38:21: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:38:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 06:38:26: 5000000 BedGraph に変換中... INFO @ Fri, 26 Jun 2020 06:38:30: 6000000 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 06:38:35: 7000000 INFO @ Fri, 26 Jun 2020 06:38:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494961/SRX494961.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494961/SRX494961.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494961/SRX494961.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494961/SRX494961.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 06:38:36: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:38:36: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:38:41: 8000000 INFO @ Fri, 26 Jun 2020 06:38:42: 1000000 INFO @ Fri, 26 Jun 2020 06:38:42: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:38:47: 9000000 INFO @ Fri, 26 Jun 2020 06:38:48: 2000000 INFO @ Fri, 26 Jun 2020 06:38:49: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 06:38:49: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 06:38:49: #1 total tags in treatment: 9420860 INFO @ Fri, 26 Jun 2020 06:38:49: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:38:49: #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 06:38:49: #1 tags after filtering in treatment: 9420860 INFO @ Fri, 26 Jun 2020 06:38:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:38:49: #1 finished! INFO @ Fri, 26 Jun 2020 06:38:49: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:38:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:38:50: #2 number of paired peaks: 1660 INFO @ Fri, 26 Jun 2020 06:38:50: start model_add_line... INFO @ Fri, 26 Jun 2020 06:38:50: start X-correlation... INFO @ Fri, 26 Jun 2020 06:38:50: end of X-cor INFO @ Fri, 26 Jun 2020 06:38:50: #2 finished! INFO @ Fri, 26 Jun 2020 06:38:50: #2 predicted fragment length is 40 bps INFO @ Fri, 26 Jun 2020 06:38:50: #2 alternative fragment length(s) may be 3,40 bps INFO @ Fri, 26 Jun 2020 06:38:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494961/SRX494961.10_model.r WARNING @ Fri, 26 Jun 2020 06:38:51: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 06:38:51: #2 You may need to consider one of the other alternative d(s): 3,40 WARNING @ Fri, 26 Jun 2020 06:38:51: #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 06:38:51: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:38:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 06:38:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494961/SRX494961.05_peaks.xls INFO @ Fri, 26 Jun 2020 06:38:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494961/SRX494961.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:38:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494961/SRX494961.05_summits.bed INFO @ Fri, 26 Jun 2020 06:38:54: Done! INFO @ Fri, 26 Jun 2020 06:38:54: 3000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4679 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 06:38:59: 4000000 INFO @ Fri, 26 Jun 2020 06:39:05: 5000000 INFO @ Fri, 26 Jun 2020 06:39:11: 6000000 INFO @ Fri, 26 Jun 2020 06:39:12: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:39:17: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 06:39:24: 8000000 INFO @ Fri, 26 Jun 2020 06:39:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494961/SRX494961.10_peaks.xls INFO @ Fri, 26 Jun 2020 06:39:30: 9000000 INFO @ Fri, 26 Jun 2020 06:39:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494961/SRX494961.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:39:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494961/SRX494961.10_summits.bed INFO @ Fri, 26 Jun 2020 06:39:31: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (1905 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 06:39:32: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 06:39:32: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 06:39:32: #1 total tags in treatment: 9420860 INFO @ Fri, 26 Jun 2020 06:39:32: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:39:32: #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 06:39:33: #1 tags after filtering in treatment: 9420860 INFO @ Fri, 26 Jun 2020 06:39:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:39:33: #1 finished! INFO @ Fri, 26 Jun 2020 06:39:33: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:39:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:39:33: #2 number of paired peaks: 1660 INFO @ Fri, 26 Jun 2020 06:39:33: start model_add_line... INFO @ Fri, 26 Jun 2020 06:39:34: start X-correlation... INFO @ Fri, 26 Jun 2020 06:39:34: end of X-cor INFO @ Fri, 26 Jun 2020 06:39:34: #2 finished! INFO @ Fri, 26 Jun 2020 06:39:34: #2 predicted fragment length is 40 bps INFO @ Fri, 26 Jun 2020 06:39:34: #2 alternative fragment length(s) may be 3,40 bps INFO @ Fri, 26 Jun 2020 06:39:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494961/SRX494961.20_model.r WARNING @ Fri, 26 Jun 2020 06:39:34: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 06:39:34: #2 You may need to consider one of the other alternative d(s): 3,40 WARNING @ Fri, 26 Jun 2020 06:39:34: #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 06:39:34: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:39:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 06:39:56: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:40:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494961/SRX494961.20_peaks.xls INFO @ Fri, 26 Jun 2020 06:40:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494961/SRX494961.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:40:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494961/SRX494961.20_summits.bed INFO @ Fri, 26 Jun 2020 06:40:08: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (600 records, 4 fields): 1 millis CompletedMACS2peakCalling