Job ID = 6458557 SRX = SRX5343092 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:41:00 prefetch.2.10.7: 1) Downloading 'SRR8540869'... 2020-06-21T12:41:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:45:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:45:11 prefetch.2.10.7: 1) 'SRR8540869' was downloaded successfully 2020-06-21T12:45:11 prefetch.2.10.7: 'SRR8540869' has 0 unresolved dependencies Read 23028434 spots for SRR8540869/SRR8540869.sra Written 23028434 spots for SRR8540869/SRR8540869.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: 00:08:44 23028434 reads; of these: 23028434 (100.00%) were unpaired; of these: 1226171 (5.32%) aligned 0 times 15004746 (65.16%) aligned exactly 1 time 6797517 (29.52%) aligned >1 times 94.68% overall alignment rate Time searching: 00:08:44 Overall time: 00:08:44 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 3307236 / 21802263 = 0.1517 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 @ Sun, 21 Jun 2020 22:03:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343092/SRX5343092.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343092/SRX5343092.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343092/SRX5343092.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343092/SRX5343092.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 @ Sun, 21 Jun 2020 22:03:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:03:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:03:44: 1000000 INFO @ Sun, 21 Jun 2020 22:03:50: 2000000 INFO @ Sun, 21 Jun 2020 22:03:55: 3000000 INFO @ Sun, 21 Jun 2020 22:04:01: 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 @ Sun, 21 Jun 2020 22:04:07: 5000000 INFO @ Sun, 21 Jun 2020 22:04:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343092/SRX5343092.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343092/SRX5343092.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343092/SRX5343092.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343092/SRX5343092.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 @ Sun, 21 Jun 2020 22:04:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:04:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:04:13: 6000000 INFO @ Sun, 21 Jun 2020 22:04:14: 1000000 INFO @ Sun, 21 Jun 2020 22:04:20: 7000000 INFO @ Sun, 21 Jun 2020 22:04:21: 2000000 INFO @ Sun, 21 Jun 2020 22:04:26: 8000000 INFO @ Sun, 21 Jun 2020 22:04:27: 3000000 INFO @ Sun, 21 Jun 2020 22:04:32: 9000000 INFO @ Sun, 21 Jun 2020 22:04:34: 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 @ Sun, 21 Jun 2020 22:04:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343092/SRX5343092.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343092/SRX5343092.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343092/SRX5343092.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343092/SRX5343092.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 @ Sun, 21 Jun 2020 22:04:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:04:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:04:39: 10000000 INFO @ Sun, 21 Jun 2020 22:04:40: 5000000 INFO @ Sun, 21 Jun 2020 22:04:45: 1000000 INFO @ Sun, 21 Jun 2020 22:04:45: 11000000 INFO @ Sun, 21 Jun 2020 22:04:47: 6000000 INFO @ Sun, 21 Jun 2020 22:04:51: 2000000 INFO @ Sun, 21 Jun 2020 22:04:52: 12000000 INFO @ Sun, 21 Jun 2020 22:04:54: 7000000 INFO @ Sun, 21 Jun 2020 22:04:58: 3000000 INFO @ Sun, 21 Jun 2020 22:04:59: 13000000 INFO @ Sun, 21 Jun 2020 22:05:00: 8000000 INFO @ Sun, 21 Jun 2020 22:05:05: 4000000 INFO @ Sun, 21 Jun 2020 22:05:05: 14000000 INFO @ Sun, 21 Jun 2020 22:05:07: 9000000 INFO @ Sun, 21 Jun 2020 22:05:11: 5000000 INFO @ Sun, 21 Jun 2020 22:05:12: 15000000 INFO @ Sun, 21 Jun 2020 22:05:13: 10000000 INFO @ Sun, 21 Jun 2020 22:05:18: 6000000 INFO @ Sun, 21 Jun 2020 22:05:19: 16000000 INFO @ Sun, 21 Jun 2020 22:05:20: 11000000 INFO @ Sun, 21 Jun 2020 22:05:24: 7000000 INFO @ Sun, 21 Jun 2020 22:05:26: 17000000 INFO @ Sun, 21 Jun 2020 22:05:26: 12000000 INFO @ Sun, 21 Jun 2020 22:05:31: 8000000 INFO @ Sun, 21 Jun 2020 22:05:32: 13000000 INFO @ Sun, 21 Jun 2020 22:05:33: 18000000 INFO @ Sun, 21 Jun 2020 22:05:36: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 22:05:36: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 22:05:36: #1 total tags in treatment: 18495027 INFO @ Sun, 21 Jun 2020 22:05:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:05:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:05:37: 9000000 INFO @ Sun, 21 Jun 2020 22:05:37: #1 tags after filtering in treatment: 18495026 INFO @ Sun, 21 Jun 2020 22:05:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:05:37: #1 finished! INFO @ Sun, 21 Jun 2020 22:05:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:05:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:05:38: #2 number of paired peaks: 258 WARNING @ Sun, 21 Jun 2020 22:05:38: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Sun, 21 Jun 2020 22:05:38: start model_add_line... INFO @ Sun, 21 Jun 2020 22:05:38: start X-correlation... INFO @ Sun, 21 Jun 2020 22:05:38: end of X-cor INFO @ Sun, 21 Jun 2020 22:05:38: #2 finished! INFO @ Sun, 21 Jun 2020 22:05:38: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 22:05:38: #2 alternative fragment length(s) may be 3,44,46 bps INFO @ Sun, 21 Jun 2020 22:05:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343092/SRX5343092.05_model.r WARNING @ Sun, 21 Jun 2020 22:05:38: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:05:38: #2 You may need to consider one of the other alternative d(s): 3,44,46 WARNING @ Sun, 21 Jun 2020 22:05:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:05:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:05:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:05:39: 14000000 INFO @ Sun, 21 Jun 2020 22:05:43: 10000000 INFO @ Sun, 21 Jun 2020 22:05:45: 15000000 INFO @ Sun, 21 Jun 2020 22:05:49: 11000000 INFO @ Sun, 21 Jun 2020 22:05:52: 16000000 INFO @ Sun, 21 Jun 2020 22:05:55: 12000000 INFO @ Sun, 21 Jun 2020 22:05:58: 17000000 INFO @ Sun, 21 Jun 2020 22:06:01: 13000000 INFO @ Sun, 21 Jun 2020 22:06:04: 18000000 INFO @ Sun, 21 Jun 2020 22:06:07: 14000000 INFO @ Sun, 21 Jun 2020 22:06:07: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 22:06:07: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 22:06:07: #1 total tags in treatment: 18495027 INFO @ Sun, 21 Jun 2020 22:06:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:06:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:06:08: #1 tags after filtering in treatment: 18495026 INFO @ Sun, 21 Jun 2020 22:06:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:06:08: #1 finished! INFO @ Sun, 21 Jun 2020 22:06:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:06:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:06:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:06:09: #2 number of paired peaks: 258 WARNING @ Sun, 21 Jun 2020 22:06:09: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Sun, 21 Jun 2020 22:06:09: start model_add_line... INFO @ Sun, 21 Jun 2020 22:06:09: start X-correlation... INFO @ Sun, 21 Jun 2020 22:06:09: end of X-cor INFO @ Sun, 21 Jun 2020 22:06:09: #2 finished! INFO @ Sun, 21 Jun 2020 22:06:09: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 22:06:09: #2 alternative fragment length(s) may be 3,44,46 bps INFO @ Sun, 21 Jun 2020 22:06:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343092/SRX5343092.10_model.r WARNING @ Sun, 21 Jun 2020 22:06:09: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:06:09: #2 You may need to consider one of the other alternative d(s): 3,44,46 WARNING @ Sun, 21 Jun 2020 22:06:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:06:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:06:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:06:13: 15000000 INFO @ Sun, 21 Jun 2020 22:06:19: 16000000 INFO @ Sun, 21 Jun 2020 22:06:24: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:06:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343092/SRX5343092.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:06:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343092/SRX5343092.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:06:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343092/SRX5343092.05_summits.bed INFO @ Sun, 21 Jun 2020 22:06:25: Done! pass1 - making usageList (710 chroms): 2 millis pass2 - checking and writing primary data (2491 records, 4 fields): 40 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:06:30: 18000000 INFO @ Sun, 21 Jun 2020 22:06:33: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 22:06:33: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 22:06:33: #1 total tags in treatment: 18495027 INFO @ Sun, 21 Jun 2020 22:06:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:06:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:06:34: #1 tags after filtering in treatment: 18495026 INFO @ Sun, 21 Jun 2020 22:06:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:06:34: #1 finished! INFO @ Sun, 21 Jun 2020 22:06:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:06:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:06:35: #2 number of paired peaks: 258 WARNING @ Sun, 21 Jun 2020 22:06:35: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Sun, 21 Jun 2020 22:06:35: start model_add_line... INFO @ Sun, 21 Jun 2020 22:06:36: start X-correlation... INFO @ Sun, 21 Jun 2020 22:06:36: end of X-cor INFO @ Sun, 21 Jun 2020 22:06:36: #2 finished! INFO @ Sun, 21 Jun 2020 22:06:36: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 22:06:36: #2 alternative fragment length(s) may be 3,44,46 bps INFO @ Sun, 21 Jun 2020 22:06:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343092/SRX5343092.20_model.r WARNING @ Sun, 21 Jun 2020 22:06:36: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:06:36: #2 You may need to consider one of the other alternative d(s): 3,44,46 WARNING @ Sun, 21 Jun 2020 22:06:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:06:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:06:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:06:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:06:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343092/SRX5343092.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:06:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343092/SRX5343092.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:06:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343092/SRX5343092.10_summits.bed INFO @ Sun, 21 Jun 2020 22:06:56: Done! pass1 - making usageList (531 chroms): 1 millis pass2 - checking and writing primary data (1530 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:07:06: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:07:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343092/SRX5343092.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:07:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343092/SRX5343092.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:07:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343092/SRX5343092.20_summits.bed INFO @ Sun, 21 Jun 2020 22:07:22: Done! pass1 - making usageList (267 chroms): 1 millis pass2 - checking and writing primary data (529 records, 4 fields): 15 millis CompletedMACS2peakCalling