Job ID = 6508753 SRX = SRX467109 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:43:22 prefetch.2.10.7: 1) Downloading 'SRR1164533'... 2020-06-26T14:43:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:44:19 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:44:20 prefetch.2.10.7: 'SRR1164533' is valid 2020-06-26T14:44:20 prefetch.2.10.7: 1) 'SRR1164533' was downloaded successfully Read 11858540 spots for SRR1164533/SRR1164533.sra Written 11858540 spots for SRR1164533/SRR1164533.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: 00:03:39 11858540 reads; of these: 11858540 (100.00%) were unpaired; of these: 701461 (5.92%) aligned 0 times 7893205 (66.56%) aligned exactly 1 time 3263874 (27.52%) aligned >1 times 94.08% overall alignment rate Time searching: 00:03:39 Overall time: 00:03:39 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 8 files... [bam_rmdupse_core] 1517628 / 11157079 = 0.1360 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 23:52:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467109/SRX467109.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467109/SRX467109.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467109/SRX467109.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467109/SRX467109.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 23:52:11: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:52:11: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:52:19: 1000000 INFO @ Fri, 26 Jun 2020 23:52:27: 2000000 INFO @ Fri, 26 Jun 2020 23:52:34: 3000000 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 23:52:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467109/SRX467109.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467109/SRX467109.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467109/SRX467109.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467109/SRX467109.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 23:52:41: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:52:41: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:52:42: 4000000 INFO @ Fri, 26 Jun 2020 23:52:50: 1000000 INFO @ Fri, 26 Jun 2020 23:52:50: 5000000 INFO @ Fri, 26 Jun 2020 23:52:58: 2000000 INFO @ Fri, 26 Jun 2020 23:52:59: 6000000 INFO @ Fri, 26 Jun 2020 23:53:06: 3000000 INFO @ Fri, 26 Jun 2020 23:53:07: 7000000 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 23:53:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX467109/SRX467109.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX467109/SRX467109.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX467109/SRX467109.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX467109/SRX467109.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 23:53:11: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:53:11: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:53:14: 4000000 INFO @ Fri, 26 Jun 2020 23:53:16: 8000000 INFO @ Fri, 26 Jun 2020 23:53:20: 1000000 INFO @ Fri, 26 Jun 2020 23:53:23: 5000000 INFO @ Fri, 26 Jun 2020 23:53:25: 9000000 INFO @ Fri, 26 Jun 2020 23:53:29: 2000000 INFO @ Fri, 26 Jun 2020 23:53:31: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:53:31: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:53:31: #1 total tags in treatment: 9639451 INFO @ Fri, 26 Jun 2020 23:53:31: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:53:31: #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 23:53:31: #1 tags after filtering in treatment: 9639446 INFO @ Fri, 26 Jun 2020 23:53:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:53:31: #1 finished! INFO @ Fri, 26 Jun 2020 23:53:31: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:53:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:53:32: 6000000 INFO @ Fri, 26 Jun 2020 23:53:32: #2 number of paired peaks: 355 WARNING @ Fri, 26 Jun 2020 23:53:32: Fewer paired peaks (355) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 355 pairs to build model! INFO @ Fri, 26 Jun 2020 23:53:32: start model_add_line... INFO @ Fri, 26 Jun 2020 23:53:32: start X-correlation... INFO @ Fri, 26 Jun 2020 23:53:32: end of X-cor INFO @ Fri, 26 Jun 2020 23:53:32: #2 finished! INFO @ Fri, 26 Jun 2020 23:53:32: #2 predicted fragment length is 78 bps INFO @ Fri, 26 Jun 2020 23:53:32: #2 alternative fragment length(s) may be 78 bps INFO @ Fri, 26 Jun 2020 23:53:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467109/SRX467109.05_model.r WARNING @ Fri, 26 Jun 2020 23:53:32: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:53:32: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Fri, 26 Jun 2020 23:53:32: #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 23:53:32: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:53:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:53:37: 3000000 INFO @ Fri, 26 Jun 2020 23:53:40: 7000000 INFO @ Fri, 26 Jun 2020 23:53:46: 4000000 INFO @ Fri, 26 Jun 2020 23:53:49: 8000000 INFO @ Fri, 26 Jun 2020 23:53:55: 5000000 INFO @ Fri, 26 Jun 2020 23:53:56: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:53:58: 9000000 INFO @ Fri, 26 Jun 2020 23:54:03: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:54:03: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:54:03: #1 total tags in treatment: 9639451 INFO @ Fri, 26 Jun 2020 23:54:03: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:54:03: #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 23:54:03: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:54:04: #1 tags after filtering in treatment: 9639446 INFO @ Fri, 26 Jun 2020 23:54:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:54:04: #1 finished! INFO @ Fri, 26 Jun 2020 23:54:04: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:54:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:54:04: #2 number of paired peaks: 355 WARNING @ Fri, 26 Jun 2020 23:54:04: Fewer paired peaks (355) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 355 pairs to build model! INFO @ Fri, 26 Jun 2020 23:54:04: start model_add_line... INFO @ Fri, 26 Jun 2020 23:54:05: start X-correlation... INFO @ Fri, 26 Jun 2020 23:54:05: end of X-cor INFO @ Fri, 26 Jun 2020 23:54:05: #2 finished! INFO @ Fri, 26 Jun 2020 23:54:05: #2 predicted fragment length is 78 bps INFO @ Fri, 26 Jun 2020 23:54:05: #2 alternative fragment length(s) may be 78 bps INFO @ Fri, 26 Jun 2020 23:54:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467109/SRX467109.10_model.r WARNING @ Fri, 26 Jun 2020 23:54:05: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:54:05: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Fri, 26 Jun 2020 23:54:05: #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 23:54:05: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:54:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:54:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467109/SRX467109.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:54:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467109/SRX467109.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:54:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467109/SRX467109.05_summits.bed INFO @ Fri, 26 Jun 2020 23:54:08: Done! pass1 - making usageList (632 chroms): 2 millis pass2 - checking and writing primary data (5546 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:54:12: 7000000 INFO @ Fri, 26 Jun 2020 23:54:20: 8000000 INFO @ Fri, 26 Jun 2020 23:54:28: 9000000 INFO @ Fri, 26 Jun 2020 23:54:28: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:54:33: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:54:33: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:54:33: #1 total tags in treatment: 9639451 INFO @ Fri, 26 Jun 2020 23:54:33: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:54:33: #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 23:54:33: #1 tags after filtering in treatment: 9639446 INFO @ Fri, 26 Jun 2020 23:54:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:54:33: #1 finished! INFO @ Fri, 26 Jun 2020 23:54:33: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:54:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:54:34: #2 number of paired peaks: 355 WARNING @ Fri, 26 Jun 2020 23:54:34: Fewer paired peaks (355) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 355 pairs to build model! INFO @ Fri, 26 Jun 2020 23:54:34: start model_add_line... INFO @ Fri, 26 Jun 2020 23:54:34: start X-correlation... INFO @ Fri, 26 Jun 2020 23:54:34: end of X-cor INFO @ Fri, 26 Jun 2020 23:54:34: #2 finished! INFO @ Fri, 26 Jun 2020 23:54:34: #2 predicted fragment length is 78 bps INFO @ Fri, 26 Jun 2020 23:54:34: #2 alternative fragment length(s) may be 78 bps INFO @ Fri, 26 Jun 2020 23:54:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX467109/SRX467109.20_model.r WARNING @ Fri, 26 Jun 2020 23:54:34: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:54:34: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Fri, 26 Jun 2020 23:54:34: #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 23:54:34: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:54:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:54:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467109/SRX467109.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:54:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467109/SRX467109.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:54:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467109/SRX467109.10_summits.bed INFO @ Fri, 26 Jun 2020 23:54:41: Done! pass1 - making usageList (439 chroms): 1 millis pass2 - checking and writing primary data (2887 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:54:57: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:55:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX467109/SRX467109.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:55:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX467109/SRX467109.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:55:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX467109/SRX467109.20_summits.bed INFO @ Fri, 26 Jun 2020 23:55:09: Done! pass1 - making usageList (180 chroms): 1 millis pass2 - checking and writing primary data (807 records, 4 fields): 8 millis CompletedMACS2peakCalling