Job ID = 6498428 SRX = SRX495285 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:35:15 prefetch.2.10.7: 1) Downloading 'SRR1198790'... 2020-06-25T23:35:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:37:16 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:37:17 prefetch.2.10.7: 'SRR1198790' is valid 2020-06-25T23:37:17 prefetch.2.10.7: 1) 'SRR1198790' was downloaded successfully Read 13102053 spots for SRR1198790/SRR1198790.sra Written 13102053 spots for SRR1198790/SRR1198790.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: 00:03:37 13102053 reads; of these: 13102053 (100.00%) were unpaired; of these: 355881 (2.72%) aligned 0 times 11026668 (84.16%) aligned exactly 1 time 1719504 (13.12%) aligned >1 times 97.28% overall alignment rate Time searching: 00:03:37 Overall time: 00:03:37 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 4664735 / 12746172 = 0.3660 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 08:44:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495285/SRX495285.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495285/SRX495285.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495285/SRX495285.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495285/SRX495285.bam'] # control file = None # effective genome size = 1.20e+08 # 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 08:44:42: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:44:42: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:44:49: 1000000 INFO @ Fri, 26 Jun 2020 08:44:56: 2000000 INFO @ Fri, 26 Jun 2020 08:45:03: 3000000 INFO @ Fri, 26 Jun 2020 08:45:09: 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 @ Fri, 26 Jun 2020 08:45:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495285/SRX495285.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495285/SRX495285.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495285/SRX495285.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495285/SRX495285.bam'] # control file = None # effective genome size = 1.20e+08 # 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 08:45:12: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:45:12: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:45:17: 5000000 INFO @ Fri, 26 Jun 2020 08:45:19: 1000000 INFO @ Fri, 26 Jun 2020 08:45:25: 6000000 INFO @ Fri, 26 Jun 2020 08:45:26: 2000000 INFO @ Fri, 26 Jun 2020 08:45:32: 7000000 INFO @ Fri, 26 Jun 2020 08:45:33: 3000000 INFO @ Fri, 26 Jun 2020 08:45:40: 4000000 INFO @ Fri, 26 Jun 2020 08:45:40: 8000000 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 08:45:41: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:45:41: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:45:41: #1 total tags in treatment: 8081437 INFO @ Fri, 26 Jun 2020 08:45:41: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:45:41: #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 08:45:41: #1 tags after filtering in treatment: 8081437 INFO @ Fri, 26 Jun 2020 08:45:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:45:41: #1 finished! INFO @ Fri, 26 Jun 2020 08:45:41: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:45:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:45:42: #2 number of paired peaks: 6648 INFO @ Fri, 26 Jun 2020 08:45:42: start model_add_line... INFO @ Fri, 26 Jun 2020 08:45:42: start X-correlation... INFO @ Fri, 26 Jun 2020 08:45:42: end of X-cor INFO @ Fri, 26 Jun 2020 08:45:42: #2 finished! INFO @ Fri, 26 Jun 2020 08:45:42: #2 predicted fragment length is 3 bps INFO @ Fri, 26 Jun 2020 08:45:42: #2 alternative fragment length(s) may be 3,10 bps INFO @ Fri, 26 Jun 2020 08:45:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495285/SRX495285.05_model.r WARNING @ Fri, 26 Jun 2020 08:45:42: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:45:42: #2 You may need to consider one of the other alternative d(s): 3,10 WARNING @ Fri, 26 Jun 2020 08:45:42: #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 08:45:42: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:45:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:45:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495285/SRX495285.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495285/SRX495285.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495285/SRX495285.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495285/SRX495285.bam'] # control file = None # effective genome size = 1.20e+08 # 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 08:45:42: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:45:42: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:45:47: 5000000 INFO @ Fri, 26 Jun 2020 08:45:50: 1000000 INFO @ Fri, 26 Jun 2020 08:45:53: 6000000 INFO @ Fri, 26 Jun 2020 08:45:57: 2000000 INFO @ Fri, 26 Jun 2020 08:45:58: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:46:00: 7000000 INFO @ Fri, 26 Jun 2020 08:46:04: 3000000 INFO @ Fri, 26 Jun 2020 08:46:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495285/SRX495285.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:46:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495285/SRX495285.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:46:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495285/SRX495285.05_summits.bed INFO @ Fri, 26 Jun 2020 08:46:06: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:46:07: 8000000 INFO @ Fri, 26 Jun 2020 08:46:07: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:46:07: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:46:07: #1 total tags in treatment: 8081437 INFO @ Fri, 26 Jun 2020 08:46:07: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:46:07: #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 08:46:07: #1 tags after filtering in treatment: 8081437 INFO @ Fri, 26 Jun 2020 08:46:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:46:07: #1 finished! INFO @ Fri, 26 Jun 2020 08:46:07: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:46:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:46:08: #2 number of paired peaks: 6648 INFO @ Fri, 26 Jun 2020 08:46:08: start model_add_line... INFO @ Fri, 26 Jun 2020 08:46:08: start X-correlation... INFO @ Fri, 26 Jun 2020 08:46:08: end of X-cor INFO @ Fri, 26 Jun 2020 08:46:08: #2 finished! INFO @ Fri, 26 Jun 2020 08:46:08: #2 predicted fragment length is 3 bps INFO @ Fri, 26 Jun 2020 08:46:08: #2 alternative fragment length(s) may be 3,10 bps INFO @ Fri, 26 Jun 2020 08:46:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495285/SRX495285.10_model.r WARNING @ Fri, 26 Jun 2020 08:46:08: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:46:08: #2 You may need to consider one of the other alternative d(s): 3,10 WARNING @ Fri, 26 Jun 2020 08:46:08: #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 08:46:08: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:46:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:46:11: 4000000 INFO @ Fri, 26 Jun 2020 08:46:17: 5000000 INFO @ Fri, 26 Jun 2020 08:46:23: 6000000 INFO @ Fri, 26 Jun 2020 08:46:25: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:46:29: 7000000 INFO @ Fri, 26 Jun 2020 08:46:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495285/SRX495285.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:46:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495285/SRX495285.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:46:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495285/SRX495285.10_summits.bed INFO @ Fri, 26 Jun 2020 08:46:32: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:46:36: 8000000 INFO @ Fri, 26 Jun 2020 08:46:36: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:46:36: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:46:36: #1 total tags in treatment: 8081437 INFO @ Fri, 26 Jun 2020 08:46:36: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:46:36: #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 08:46:36: #1 tags after filtering in treatment: 8081437 INFO @ Fri, 26 Jun 2020 08:46:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:46:36: #1 finished! INFO @ Fri, 26 Jun 2020 08:46:36: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:46:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:46:37: #2 number of paired peaks: 6648 INFO @ Fri, 26 Jun 2020 08:46:37: start model_add_line... INFO @ Fri, 26 Jun 2020 08:46:37: start X-correlation... INFO @ Fri, 26 Jun 2020 08:46:37: end of X-cor INFO @ Fri, 26 Jun 2020 08:46:37: #2 finished! INFO @ Fri, 26 Jun 2020 08:46:37: #2 predicted fragment length is 3 bps INFO @ Fri, 26 Jun 2020 08:46:37: #2 alternative fragment length(s) may be 3,10 bps INFO @ Fri, 26 Jun 2020 08:46:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495285/SRX495285.20_model.r WARNING @ Fri, 26 Jun 2020 08:46:37: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:46:37: #2 You may need to consider one of the other alternative d(s): 3,10 WARNING @ Fri, 26 Jun 2020 08:46:37: #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 08:46:37: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:46:37: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:46:54: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:47:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495285/SRX495285.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:47:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495285/SRX495285.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:47:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495285/SRX495285.20_summits.bed INFO @ Fri, 26 Jun 2020 08:47:02: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling