Job ID = 6498401 SRX = SRX495236 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:36:31 prefetch.2.10.7: 1) Downloading 'SRR1198741'... 2020-06-25T23:36:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:39:59 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:39:59 prefetch.2.10.7: 1) 'SRR1198741' was downloaded successfully Read 22005854 spots for SRR1198741/SRR1198741.sra Written 22005854 spots for SRR1198741/SRR1198741.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: 00:04:00 22005854 reads; of these: 22005854 (100.00%) were unpaired; of these: 2578965 (11.72%) aligned 0 times 17817673 (80.97%) aligned exactly 1 time 1609216 (7.31%) aligned >1 times 88.28% overall alignment rate Time searching: 00:04:00 Overall time: 00:04:00 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] 7661202 / 19426889 = 0.3944 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 08:50:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495236/SRX495236.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495236/SRX495236.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495236/SRX495236.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495236/SRX495236.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 08:50:14: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:50:14: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:50:19: 1000000 INFO @ Fri, 26 Jun 2020 08:50:24: 2000000 INFO @ Fri, 26 Jun 2020 08:50:29: 3000000 INFO @ Fri, 26 Jun 2020 08:50:34: 4000000 INFO @ Fri, 26 Jun 2020 08:50:39: 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 08:50:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495236/SRX495236.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495236/SRX495236.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495236/SRX495236.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495236/SRX495236.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 08:50:44: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:50:44: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:50:44: 6000000 INFO @ Fri, 26 Jun 2020 08:50:49: 1000000 INFO @ Fri, 26 Jun 2020 08:50:49: 7000000 INFO @ Fri, 26 Jun 2020 08:50:54: 2000000 INFO @ Fri, 26 Jun 2020 08:50:54: 8000000 INFO @ Fri, 26 Jun 2020 08:50:59: 3000000 INFO @ Fri, 26 Jun 2020 08:50:59: 9000000 INFO @ Fri, 26 Jun 2020 08:51:04: 4000000 INFO @ Fri, 26 Jun 2020 08:51:04: 10000000 INFO @ Fri, 26 Jun 2020 08:51:09: 5000000 INFO @ Fri, 26 Jun 2020 08:51:10: 11000000 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 08:51:13: 6000000 INFO @ Fri, 26 Jun 2020 08:51:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495236/SRX495236.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495236/SRX495236.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495236/SRX495236.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495236/SRX495236.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 08:51:14: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:51:14: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:51:14: #1 tag size is determined as 44 bps INFO @ Fri, 26 Jun 2020 08:51:14: #1 tag size = 44 INFO @ Fri, 26 Jun 2020 08:51:14: #1 total tags in treatment: 11765687 INFO @ Fri, 26 Jun 2020 08:51:14: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:51:14: #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 08:51:14: #1 tags after filtering in treatment: 11765687 INFO @ Fri, 26 Jun 2020 08:51:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:51:14: #1 finished! INFO @ Fri, 26 Jun 2020 08:51:14: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:51:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:51:15: #2 number of paired peaks: 5499 INFO @ Fri, 26 Jun 2020 08:51:15: start model_add_line... INFO @ Fri, 26 Jun 2020 08:51:16: start X-correlation... INFO @ Fri, 26 Jun 2020 08:51:16: end of X-cor INFO @ Fri, 26 Jun 2020 08:51:16: #2 finished! INFO @ Fri, 26 Jun 2020 08:51:16: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 08:51:16: #2 alternative fragment length(s) may be 1 bps INFO @ Fri, 26 Jun 2020 08:51:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495236/SRX495236.05_model.r WARNING @ Fri, 26 Jun 2020 08:51:16: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:51:16: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Fri, 26 Jun 2020 08:51:16: #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 08:51:16: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:51:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:51:19: 7000000 INFO @ Fri, 26 Jun 2020 08:51:19: 1000000 INFO @ Fri, 26 Jun 2020 08:51:24: 8000000 INFO @ Fri, 26 Jun 2020 08:51:24: 2000000 INFO @ Fri, 26 Jun 2020 08:51:29: 9000000 INFO @ Fri, 26 Jun 2020 08:51:29: 3000000 INFO @ Fri, 26 Jun 2020 08:51:34: 10000000 INFO @ Fri, 26 Jun 2020 08:51:34: 4000000 INFO @ Fri, 26 Jun 2020 08:51:35: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:51:39: 11000000 INFO @ Fri, 26 Jun 2020 08:51:39: 5000000 INFO @ Fri, 26 Jun 2020 08:51:43: #1 tag size is determined as 44 bps INFO @ Fri, 26 Jun 2020 08:51:43: #1 tag size = 44 INFO @ Fri, 26 Jun 2020 08:51:43: #1 total tags in treatment: 11765687 INFO @ Fri, 26 Jun 2020 08:51:43: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:51:43: #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 08:51:44: #1 tags after filtering in treatment: 11765687 INFO @ Fri, 26 Jun 2020 08:51:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:51:44: #1 finished! INFO @ Fri, 26 Jun 2020 08:51:44: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:51:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:51:44: 6000000 INFO @ Fri, 26 Jun 2020 08:51:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495236/SRX495236.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:51:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495236/SRX495236.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:51:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495236/SRX495236.05_summits.bed INFO @ Fri, 26 Jun 2020 08:51:45: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:51:45: #2 number of paired peaks: 5499 INFO @ Fri, 26 Jun 2020 08:51:45: start model_add_line... INFO @ Fri, 26 Jun 2020 08:51:45: start X-correlation... INFO @ Fri, 26 Jun 2020 08:51:45: end of X-cor INFO @ Fri, 26 Jun 2020 08:51:45: #2 finished! INFO @ Fri, 26 Jun 2020 08:51:45: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 08:51:45: #2 alternative fragment length(s) may be 1 bps INFO @ Fri, 26 Jun 2020 08:51:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495236/SRX495236.10_model.r WARNING @ Fri, 26 Jun 2020 08:51:45: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:51:45: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Fri, 26 Jun 2020 08:51:45: #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 08:51:45: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:51:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:51:49: 7000000 INFO @ Fri, 26 Jun 2020 08:51:54: 8000000 INFO @ Fri, 26 Jun 2020 08:51:59: 9000000 INFO @ Fri, 26 Jun 2020 08:52:04: 10000000 INFO @ Fri, 26 Jun 2020 08:52:04: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:52:08: 11000000 INFO @ Fri, 26 Jun 2020 08:52:12: #1 tag size is determined as 44 bps INFO @ Fri, 26 Jun 2020 08:52:12: #1 tag size = 44 INFO @ Fri, 26 Jun 2020 08:52:12: #1 total tags in treatment: 11765687 INFO @ Fri, 26 Jun 2020 08:52:12: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:52:12: #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 08:52:12: #1 tags after filtering in treatment: 11765687 INFO @ Fri, 26 Jun 2020 08:52:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:52:12: #1 finished! INFO @ Fri, 26 Jun 2020 08:52:12: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:52:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:52:14: #2 number of paired peaks: 5499 INFO @ Fri, 26 Jun 2020 08:52:14: start model_add_line... INFO @ Fri, 26 Jun 2020 08:52:14: start X-correlation... INFO @ Fri, 26 Jun 2020 08:52:14: end of X-cor INFO @ Fri, 26 Jun 2020 08:52:14: #2 finished! INFO @ Fri, 26 Jun 2020 08:52:14: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 08:52:14: #2 alternative fragment length(s) may be 1 bps INFO @ Fri, 26 Jun 2020 08:52:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495236/SRX495236.20_model.r WARNING @ Fri, 26 Jun 2020 08:52:14: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:52:14: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Fri, 26 Jun 2020 08:52:14: #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 08:52:14: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:52:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:52:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495236/SRX495236.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:52:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495236/SRX495236.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:52:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495236/SRX495236.10_summits.bed INFO @ Fri, 26 Jun 2020 08:52:14: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:52:33: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:52:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495236/SRX495236.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:52:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495236/SRX495236.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:52:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495236/SRX495236.20_summits.bed INFO @ Fri, 26 Jun 2020 08:52:42: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。