Job ID = 6498029 SRX = SRX287902 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:13:19 prefetch.2.10.7: 1) Downloading 'SRR870091'... 2020-06-25T23:13:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:14:48 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:14:49 prefetch.2.10.7: 'SRR870091' is valid 2020-06-25T23:14:49 prefetch.2.10.7: 1) 'SRR870091' was downloaded successfully Read 13389851 spots for SRR870091/SRR870091.sra Written 13389851 spots for SRR870091/SRR870091.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: 00:05:47 13389851 reads; of these: 13389851 (100.00%) were unpaired; of these: 780831 (5.83%) aligned 0 times 8324656 (62.17%) aligned exactly 1 time 4284364 (32.00%) aligned >1 times 94.17% overall alignment rate Time searching: 00:05:47 Overall time: 00:05:47 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] 1579419 / 12609020 = 0.1253 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 08:25:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287902/SRX287902.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287902/SRX287902.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287902/SRX287902.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287902/SRX287902.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 08:25:37: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:25:37: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:25:43: 1000000 INFO @ Fri, 26 Jun 2020 08:25:49: 2000000 INFO @ Fri, 26 Jun 2020 08:25:55: 3000000 INFO @ Fri, 26 Jun 2020 08:26:01: 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 08:26:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287902/SRX287902.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287902/SRX287902.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287902/SRX287902.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287902/SRX287902.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 08:26:07: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:26:07: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:26:07: 5000000 INFO @ Fri, 26 Jun 2020 08:26:13: 1000000 INFO @ Fri, 26 Jun 2020 08:26:14: 6000000 INFO @ Fri, 26 Jun 2020 08:26:19: 2000000 INFO @ Fri, 26 Jun 2020 08:26:20: 7000000 INFO @ Fri, 26 Jun 2020 08:26:26: 3000000 INFO @ Fri, 26 Jun 2020 08:26:26: 8000000 INFO @ Fri, 26 Jun 2020 08:26:32: 4000000 INFO @ Fri, 26 Jun 2020 08:26:32: 9000000 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 08:26:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287902/SRX287902.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287902/SRX287902.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287902/SRX287902.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287902/SRX287902.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 08:26:37: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:26:37: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:26:38: 5000000 INFO @ Fri, 26 Jun 2020 08:26:38: 10000000 INFO @ Fri, 26 Jun 2020 08:26:44: 1000000 INFO @ Fri, 26 Jun 2020 08:26:44: 11000000 INFO @ Fri, 26 Jun 2020 08:26:45: 6000000 INFO @ Fri, 26 Jun 2020 08:26:45: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:26:45: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:26:45: #1 total tags in treatment: 11029601 INFO @ Fri, 26 Jun 2020 08:26:45: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:26:45: #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 08:26:45: #1 tags after filtering in treatment: 11029601 INFO @ Fri, 26 Jun 2020 08:26:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:26:45: #1 finished! INFO @ Fri, 26 Jun 2020 08:26:45: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:26:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:26:46: #2 number of paired peaks: 493 WARNING @ Fri, 26 Jun 2020 08:26:46: Fewer paired peaks (493) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 493 pairs to build model! INFO @ Fri, 26 Jun 2020 08:26:46: start model_add_line... INFO @ Fri, 26 Jun 2020 08:26:46: start X-correlation... INFO @ Fri, 26 Jun 2020 08:26:46: end of X-cor INFO @ Fri, 26 Jun 2020 08:26:46: #2 finished! INFO @ Fri, 26 Jun 2020 08:26:46: #2 predicted fragment length is 46 bps INFO @ Fri, 26 Jun 2020 08:26:46: #2 alternative fragment length(s) may be 46 bps INFO @ Fri, 26 Jun 2020 08:26:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287902/SRX287902.05_model.r WARNING @ Fri, 26 Jun 2020 08:26:46: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:26:46: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Fri, 26 Jun 2020 08:26:46: #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 08:26:46: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:26:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:26:51: 2000000 INFO @ Fri, 26 Jun 2020 08:26:51: 7000000 INFO @ Fri, 26 Jun 2020 08:26:57: 8000000 INFO @ Fri, 26 Jun 2020 08:26:58: 3000000 INFO @ Fri, 26 Jun 2020 08:27:03: 9000000 INFO @ Fri, 26 Jun 2020 08:27:05: 4000000 INFO @ Fri, 26 Jun 2020 08:27:09: 10000000 INFO @ Fri, 26 Jun 2020 08:27:12: 5000000 INFO @ Fri, 26 Jun 2020 08:27:12: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:27:15: 11000000 INFO @ Fri, 26 Jun 2020 08:27:16: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:27:16: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:27:16: #1 total tags in treatment: 11029601 INFO @ Fri, 26 Jun 2020 08:27:16: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:27:16: #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 08:27:16: #1 tags after filtering in treatment: 11029601 INFO @ Fri, 26 Jun 2020 08:27:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:27:16: #1 finished! INFO @ Fri, 26 Jun 2020 08:27:16: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:27:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:27:17: #2 number of paired peaks: 493 WARNING @ Fri, 26 Jun 2020 08:27:17: Fewer paired peaks (493) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 493 pairs to build model! INFO @ Fri, 26 Jun 2020 08:27:17: start model_add_line... INFO @ Fri, 26 Jun 2020 08:27:17: start X-correlation... INFO @ Fri, 26 Jun 2020 08:27:17: end of X-cor INFO @ Fri, 26 Jun 2020 08:27:17: #2 finished! INFO @ Fri, 26 Jun 2020 08:27:17: #2 predicted fragment length is 46 bps INFO @ Fri, 26 Jun 2020 08:27:17: #2 alternative fragment length(s) may be 46 bps INFO @ Fri, 26 Jun 2020 08:27:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287902/SRX287902.10_model.r WARNING @ Fri, 26 Jun 2020 08:27:17: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:27:17: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Fri, 26 Jun 2020 08:27:17: #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 08:27:17: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:27:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:27:18: 6000000 INFO @ Fri, 26 Jun 2020 08:27:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287902/SRX287902.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:27:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287902/SRX287902.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:27:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287902/SRX287902.05_summits.bed INFO @ Fri, 26 Jun 2020 08:27:25: Done! INFO @ Fri, 26 Jun 2020 08:27:25: 7000000 pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2058 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:27:32: 8000000 INFO @ Fri, 26 Jun 2020 08:27:38: 9000000 INFO @ Fri, 26 Jun 2020 08:27:43: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:27:45: 10000000 INFO @ Fri, 26 Jun 2020 08:27:51: 11000000 INFO @ Fri, 26 Jun 2020 08:27:51: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:27:51: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:27:51: #1 total tags in treatment: 11029601 INFO @ Fri, 26 Jun 2020 08:27:51: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:27:51: #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 08:27:52: #1 tags after filtering in treatment: 11029601 INFO @ Fri, 26 Jun 2020 08:27:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:27:52: #1 finished! INFO @ Fri, 26 Jun 2020 08:27:52: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:27:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:27:52: #2 number of paired peaks: 493 WARNING @ Fri, 26 Jun 2020 08:27:52: Fewer paired peaks (493) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 493 pairs to build model! INFO @ Fri, 26 Jun 2020 08:27:52: start model_add_line... INFO @ Fri, 26 Jun 2020 08:27:53: start X-correlation... INFO @ Fri, 26 Jun 2020 08:27:53: end of X-cor INFO @ Fri, 26 Jun 2020 08:27:53: #2 finished! INFO @ Fri, 26 Jun 2020 08:27:53: #2 predicted fragment length is 46 bps INFO @ Fri, 26 Jun 2020 08:27:53: #2 alternative fragment length(s) may be 46 bps INFO @ Fri, 26 Jun 2020 08:27:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287902/SRX287902.20_model.r WARNING @ Fri, 26 Jun 2020 08:27:53: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:27:53: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Fri, 26 Jun 2020 08:27:53: #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 08:27:53: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:27:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:27:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287902/SRX287902.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:27:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287902/SRX287902.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:27:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287902/SRX287902.10_summits.bed INFO @ Fri, 26 Jun 2020 08:27:56: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1785 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:28:18: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:28:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287902/SRX287902.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:28:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287902/SRX287902.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:28:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287902/SRX287902.20_summits.bed INFO @ Fri, 26 Jun 2020 08:28:31: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1356 records, 4 fields): 3 millis CompletedMACS2peakCalling