Job ID = 6498297 SRX = SRX467108 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:34:30 prefetch.2.10.7: 1) Downloading 'SRR1164532'... 2020-06-25T23:34:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:37:14 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:37:14 prefetch.2.10.7: 1) 'SRR1164532' was downloaded successfully Read 18433026 spots for SRR1164532/SRR1164532.sra Written 18433026 spots for SRR1164532/SRR1164532.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: 00:07:26 18433026 reads; of these: 18433026 (100.00%) were unpaired; of these: 2118579 (11.49%) aligned 0 times 11473064 (62.24%) aligned exactly 1 time 4841383 (26.26%) aligned >1 times 88.51% overall alignment rate Time searching: 00:07:26 Overall time: 00:07:26 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] 3103606 / 16314447 = 0.1902 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 08:50:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467108/SRX467108.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467108/SRX467108.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467108/SRX467108.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467108/SRX467108.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 08:50:08: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:50:08: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:50:15: 1000000 INFO @ Fri, 26 Jun 2020 08:50:22: 2000000 INFO @ Fri, 26 Jun 2020 08:50:28: 3000000 INFO @ Fri, 26 Jun 2020 08:50:35: 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 08:50:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467108/SRX467108.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467108/SRX467108.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467108/SRX467108.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467108/SRX467108.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 08:50:38: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:50:38: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:50:42: 5000000 INFO @ Fri, 26 Jun 2020 08:50:45: 1000000 INFO @ Fri, 26 Jun 2020 08:50:48: 6000000 INFO @ Fri, 26 Jun 2020 08:50:52: 2000000 INFO @ Fri, 26 Jun 2020 08:50:55: 7000000 INFO @ Fri, 26 Jun 2020 08:50:58: 3000000 INFO @ Fri, 26 Jun 2020 08:51:02: 8000000 INFO @ Fri, 26 Jun 2020 08:51:05: 4000000 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 08:51:08: 9000000 INFO @ Fri, 26 Jun 2020 08:51:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467108/SRX467108.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467108/SRX467108.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467108/SRX467108.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467108/SRX467108.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 08:51:08: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:51:08: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:51:12: 5000000 INFO @ Fri, 26 Jun 2020 08:51:15: 1000000 INFO @ Fri, 26 Jun 2020 08:51:15: 10000000 INFO @ Fri, 26 Jun 2020 08:51:18: 6000000 INFO @ Fri, 26 Jun 2020 08:51:21: 2000000 INFO @ Fri, 26 Jun 2020 08:51:22: 11000000 INFO @ Fri, 26 Jun 2020 08:51:25: 7000000 INFO @ Fri, 26 Jun 2020 08:51:28: 3000000 INFO @ Fri, 26 Jun 2020 08:51:29: 12000000 INFO @ Fri, 26 Jun 2020 08:51:31: 8000000 INFO @ Fri, 26 Jun 2020 08:51:34: 4000000 INFO @ Fri, 26 Jun 2020 08:51:36: 13000000 INFO @ Fri, 26 Jun 2020 08:51:38: 9000000 INFO @ Fri, 26 Jun 2020 08:51:38: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:51:38: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:51:38: #1 total tags in treatment: 13210841 INFO @ Fri, 26 Jun 2020 08:51:38: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:51:38: #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 08:51:38: #1 tags after filtering in treatment: 13210841 INFO @ Fri, 26 Jun 2020 08:51:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:51:38: #1 finished! INFO @ Fri, 26 Jun 2020 08:51:38: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:51:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:51:39: #2 number of paired peaks: 358 WARNING @ Fri, 26 Jun 2020 08:51:39: Fewer paired peaks (358) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 358 pairs to build model! INFO @ Fri, 26 Jun 2020 08:51:39: start model_add_line... INFO @ Fri, 26 Jun 2020 08:51:39: start X-correlation... INFO @ Fri, 26 Jun 2020 08:51:39: end of X-cor INFO @ Fri, 26 Jun 2020 08:51:39: #2 finished! INFO @ Fri, 26 Jun 2020 08:51:39: #2 predicted fragment length is 45 bps INFO @ Fri, 26 Jun 2020 08:51:39: #2 alternative fragment length(s) may be 45 bps INFO @ Fri, 26 Jun 2020 08:51:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467108/SRX467108.05_model.r WARNING @ Fri, 26 Jun 2020 08:51:39: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:51:39: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Fri, 26 Jun 2020 08:51:39: #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 08:51:39: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:51:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:51:40: 5000000 INFO @ Fri, 26 Jun 2020 08:51:45: 10000000 INFO @ Fri, 26 Jun 2020 08:51:46: 6000000 INFO @ Fri, 26 Jun 2020 08:51:51: 11000000 INFO @ Fri, 26 Jun 2020 08:51:52: 7000000 INFO @ Fri, 26 Jun 2020 08:51:58: 12000000 INFO @ Fri, 26 Jun 2020 08:51:58: 8000000 INFO @ Fri, 26 Jun 2020 08:52:05: 9000000 INFO @ Fri, 26 Jun 2020 08:52:05: 13000000 INFO @ Fri, 26 Jun 2020 08:52:06: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:52:06: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:52:06: #1 total tags in treatment: 13210841 INFO @ Fri, 26 Jun 2020 08:52:06: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:52:06: #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 08:52:06: #1 tags after filtering in treatment: 13210841 INFO @ Fri, 26 Jun 2020 08:52:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:52:06: #1 finished! INFO @ Fri, 26 Jun 2020 08:52:06: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:52:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:52:08: #2 number of paired peaks: 358 WARNING @ Fri, 26 Jun 2020 08:52:08: Fewer paired peaks (358) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 358 pairs to build model! INFO @ Fri, 26 Jun 2020 08:52:08: start model_add_line... INFO @ Fri, 26 Jun 2020 08:52:08: start X-correlation... INFO @ Fri, 26 Jun 2020 08:52:08: end of X-cor INFO @ Fri, 26 Jun 2020 08:52:08: #2 finished! INFO @ Fri, 26 Jun 2020 08:52:08: #2 predicted fragment length is 45 bps INFO @ Fri, 26 Jun 2020 08:52:08: #2 alternative fragment length(s) may be 45 bps INFO @ Fri, 26 Jun 2020 08:52:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467108/SRX467108.10_model.r WARNING @ Fri, 26 Jun 2020 08:52:08: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:52:08: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Fri, 26 Jun 2020 08:52:08: #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 08:52:08: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:52:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:52:08: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:52:10: 10000000 INFO @ Fri, 26 Jun 2020 08:52:16: 11000000 INFO @ Fri, 26 Jun 2020 08:52:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467108/SRX467108.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:52:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467108/SRX467108.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:52:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467108/SRX467108.05_summits.bed INFO @ Fri, 26 Jun 2020 08:52:22: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2135 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:52:22: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:52:28: 13000000 INFO @ Fri, 26 Jun 2020 08:52:29: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:52:29: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:52:29: #1 total tags in treatment: 13210841 INFO @ Fri, 26 Jun 2020 08:52:29: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:52:29: #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 08:52:30: #1 tags after filtering in treatment: 13210841 INFO @ Fri, 26 Jun 2020 08:52:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:52:30: #1 finished! INFO @ Fri, 26 Jun 2020 08:52:30: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:52:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:52:31: #2 number of paired peaks: 358 WARNING @ Fri, 26 Jun 2020 08:52:31: Fewer paired peaks (358) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 358 pairs to build model! INFO @ Fri, 26 Jun 2020 08:52:31: start model_add_line... INFO @ Fri, 26 Jun 2020 08:52:31: start X-correlation... INFO @ Fri, 26 Jun 2020 08:52:31: end of X-cor INFO @ Fri, 26 Jun 2020 08:52:31: #2 finished! INFO @ Fri, 26 Jun 2020 08:52:31: #2 predicted fragment length is 45 bps INFO @ Fri, 26 Jun 2020 08:52:31: #2 alternative fragment length(s) may be 45 bps INFO @ Fri, 26 Jun 2020 08:52:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467108/SRX467108.20_model.r WARNING @ Fri, 26 Jun 2020 08:52:31: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:52:31: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Fri, 26 Jun 2020 08:52:31: #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 08:52:31: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:52:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:52:36: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:52:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467108/SRX467108.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:52:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467108/SRX467108.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:52:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467108/SRX467108.10_summits.bed INFO @ Fri, 26 Jun 2020 08:52:49: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1753 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:52:59: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:53:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467108/SRX467108.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:53:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467108/SRX467108.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:53:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467108/SRX467108.20_summits.bed INFO @ Fri, 26 Jun 2020 08:53:13: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1256 records, 4 fields): 3 millis CompletedMACS2peakCalling