Job ID = 6498429 SRX = SRX495286 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:41:06 prefetch.2.10.7: 1) Downloading 'SRR1198791'... 2020-06-25T23:41:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:42:47 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:42:48 prefetch.2.10.7: 'SRR1198791' is valid 2020-06-25T23:42:48 prefetch.2.10.7: 1) 'SRR1198791' was downloaded successfully Read 13356499 spots for SRR1198791/SRR1198791.sra Written 13356499 spots for SRR1198791/SRR1198791.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: 00:03:25 13356499 reads; of these: 13356499 (100.00%) were unpaired; of these: 278734 (2.09%) aligned 0 times 11628791 (87.06%) aligned exactly 1 time 1448974 (10.85%) aligned >1 times 97.91% overall alignment rate Time searching: 00:03:25 Overall time: 00:03:25 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] 3913994 / 13077765 = 0.2993 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 08:50:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495286/SRX495286.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495286/SRX495286.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495286/SRX495286.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495286/SRX495286.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 08:50:26: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:50:26: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:50:32: 1000000 INFO @ Fri, 26 Jun 2020 08:50:38: 2000000 INFO @ Fri, 26 Jun 2020 08:50:43: 3000000 INFO @ Fri, 26 Jun 2020 08:50:49: 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 08:50:55: 5000000 INFO @ Fri, 26 Jun 2020 08:50:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495286/SRX495286.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495286/SRX495286.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495286/SRX495286.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495286/SRX495286.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 08:50:56: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:50:56: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:51:01: 6000000 INFO @ Fri, 26 Jun 2020 08:51:02: 1000000 INFO @ Fri, 26 Jun 2020 08:51:07: 7000000 INFO @ Fri, 26 Jun 2020 08:51:07: 2000000 INFO @ Fri, 26 Jun 2020 08:51:14: 3000000 INFO @ Fri, 26 Jun 2020 08:51:14: 8000000 INFO @ Fri, 26 Jun 2020 08:51:20: 4000000 INFO @ Fri, 26 Jun 2020 08:51:20: 9000000 INFO @ Fri, 26 Jun 2020 08:51:21: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:51:21: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:51:21: #1 total tags in treatment: 9163771 INFO @ Fri, 26 Jun 2020 08:51:21: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:51:21: #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 08:51:21: #1 tags after filtering in treatment: 9163771 INFO @ Fri, 26 Jun 2020 08:51:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:51:21: #1 finished! INFO @ Fri, 26 Jun 2020 08:51:21: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:51:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:51:22: #2 number of paired peaks: 4315 INFO @ Fri, 26 Jun 2020 08:51:22: start model_add_line... INFO @ Fri, 26 Jun 2020 08:51:22: start X-correlation... INFO @ Fri, 26 Jun 2020 08:51:22: end of X-cor INFO @ Fri, 26 Jun 2020 08:51:22: #2 finished! INFO @ Fri, 26 Jun 2020 08:51:22: #2 predicted fragment length is 3 bps INFO @ Fri, 26 Jun 2020 08:51:22: #2 alternative fragment length(s) may be 3,11 bps INFO @ Fri, 26 Jun 2020 08:51:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495286/SRX495286.05_model.r WARNING @ Fri, 26 Jun 2020 08:51:22: #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 08:51:22: #2 You may need to consider one of the other alternative d(s): 3,11 WARNING @ Fri, 26 Jun 2020 08:51:22: #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 08:51:22: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:51:22: #3 Pre-compute pvalue-qvalue table... 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 08:51:26: 5000000 INFO @ Fri, 26 Jun 2020 08:51:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495286/SRX495286.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495286/SRX495286.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495286/SRX495286.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495286/SRX495286.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 08:51:26: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:51:26: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:51:32: 6000000 INFO @ Fri, 26 Jun 2020 08:51:32: 1000000 INFO @ Fri, 26 Jun 2020 08:51:38: 2000000 INFO @ Fri, 26 Jun 2020 08:51:38: 7000000 INFO @ Fri, 26 Jun 2020 08:51:42: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:51:44: 3000000 INFO @ Fri, 26 Jun 2020 08:51:44: 8000000 INFO @ Fri, 26 Jun 2020 08:51:50: 4000000 INFO @ Fri, 26 Jun 2020 08:51:50: 9000000 INFO @ Fri, 26 Jun 2020 08:51:51: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:51:51: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:51:51: #1 total tags in treatment: 9163771 INFO @ Fri, 26 Jun 2020 08:51:51: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:51:51: #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 08:51:51: #1 tags after filtering in treatment: 9163771 INFO @ Fri, 26 Jun 2020 08:51:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:51:51: #1 finished! INFO @ Fri, 26 Jun 2020 08:51:51: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:51:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:51:52: #2 number of paired peaks: 4315 INFO @ Fri, 26 Jun 2020 08:51:52: start model_add_line... INFO @ Fri, 26 Jun 2020 08:51:52: start X-correlation... INFO @ Fri, 26 Jun 2020 08:51:52: end of X-cor INFO @ Fri, 26 Jun 2020 08:51:52: #2 finished! INFO @ Fri, 26 Jun 2020 08:51:52: #2 predicted fragment length is 3 bps INFO @ Fri, 26 Jun 2020 08:51:52: #2 alternative fragment length(s) may be 3,11 bps INFO @ Fri, 26 Jun 2020 08:51:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495286/SRX495286.10_model.r WARNING @ Fri, 26 Jun 2020 08:51:52: #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 08:51:52: #2 You may need to consider one of the other alternative d(s): 3,11 WARNING @ Fri, 26 Jun 2020 08:51:52: #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 08:51:52: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:51:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:51:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495286/SRX495286.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:51:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495286/SRX495286.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:51:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495286/SRX495286.05_summits.bed INFO @ Fri, 26 Jun 2020 08:51:53: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:51:56: 5000000 INFO @ Fri, 26 Jun 2020 08:52:01: 6000000 INFO @ Fri, 26 Jun 2020 08:52:07: 7000000 INFO @ Fri, 26 Jun 2020 08:52:13: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:52:13: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:52:19: 9000000 INFO @ Fri, 26 Jun 2020 08:52:20: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:52:20: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:52:20: #1 total tags in treatment: 9163771 INFO @ Fri, 26 Jun 2020 08:52:20: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:52:20: #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 08:52:20: #1 tags after filtering in treatment: 9163771 INFO @ Fri, 26 Jun 2020 08:52:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:52:20: #1 finished! INFO @ Fri, 26 Jun 2020 08:52:20: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:52:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:52:21: #2 number of paired peaks: 4315 INFO @ Fri, 26 Jun 2020 08:52:21: start model_add_line... INFO @ Fri, 26 Jun 2020 08:52:21: start X-correlation... INFO @ Fri, 26 Jun 2020 08:52:21: end of X-cor INFO @ Fri, 26 Jun 2020 08:52:21: #2 finished! INFO @ Fri, 26 Jun 2020 08:52:21: #2 predicted fragment length is 3 bps INFO @ Fri, 26 Jun 2020 08:52:21: #2 alternative fragment length(s) may be 3,11 bps INFO @ Fri, 26 Jun 2020 08:52:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495286/SRX495286.20_model.r WARNING @ Fri, 26 Jun 2020 08:52:21: #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 08:52:21: #2 You may need to consider one of the other alternative d(s): 3,11 WARNING @ Fri, 26 Jun 2020 08:52:21: #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 08:52:21: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:52:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:52:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495286/SRX495286.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:52:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495286/SRX495286.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:52:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495286/SRX495286.10_summits.bed INFO @ Fri, 26 Jun 2020 08:52:23: 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。 INFO @ Fri, 26 Jun 2020 08:52:40: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:52:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495286/SRX495286.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:52:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495286/SRX495286.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:52:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495286/SRX495286.20_summits.bed INFO @ Fri, 26 Jun 2020 08:52:51: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling