Job ID = 6455897 SRX = SRX306190 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:17:36 prefetch.2.10.7: 1) Downloading 'SRR901293'... 2020-06-21T10:17:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:23:05 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:23:05 prefetch.2.10.7: 1) 'SRR901293' was downloaded successfully Read 34066666 spots for SRR901293/SRR901293.sra Written 34066666 spots for SRR901293/SRR901293.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: 00:00:01 Multiseed full-index search: 00:10:15 34066666 reads; of these: 34066666 (100.00%) were unpaired; of these: 2359301 (6.93%) aligned 0 times 23377738 (68.62%) aligned exactly 1 time 8329627 (24.45%) aligned >1 times 93.07% overall alignment rate Time searching: 00:10:16 Overall time: 00:10:16 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 16 files... [bam_rmdupse_core] 4609490 / 31707365 = 0.1454 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 19:44:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX306190/SRX306190.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX306190/SRX306190.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX306190/SRX306190.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX306190/SRX306190.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 19:44:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:44:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:44:17: 1000000 INFO @ Sun, 21 Jun 2020 19:44:23: 2000000 INFO @ Sun, 21 Jun 2020 19:44:29: 3000000 INFO @ Sun, 21 Jun 2020 19:44:35: 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 @ Sun, 21 Jun 2020 19:44:41: 5000000 INFO @ Sun, 21 Jun 2020 19:44:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX306190/SRX306190.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX306190/SRX306190.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX306190/SRX306190.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX306190/SRX306190.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 19:44:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:44:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:44:47: 6000000 INFO @ Sun, 21 Jun 2020 19:44:48: 1000000 INFO @ Sun, 21 Jun 2020 19:44:54: 7000000 INFO @ Sun, 21 Jun 2020 19:44:54: 2000000 INFO @ Sun, 21 Jun 2020 19:45:00: 8000000 INFO @ Sun, 21 Jun 2020 19:45:01: 3000000 INFO @ Sun, 21 Jun 2020 19:45:06: 9000000 INFO @ Sun, 21 Jun 2020 19:45:07: 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 19:45:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX306190/SRX306190.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX306190/SRX306190.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX306190/SRX306190.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX306190/SRX306190.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 19:45:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:45:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:45:12: 10000000 INFO @ Sun, 21 Jun 2020 19:45:13: 5000000 INFO @ Sun, 21 Jun 2020 19:45:17: 1000000 INFO @ Sun, 21 Jun 2020 19:45:19: 11000000 INFO @ Sun, 21 Jun 2020 19:45:19: 6000000 INFO @ Sun, 21 Jun 2020 19:45:23: 2000000 INFO @ Sun, 21 Jun 2020 19:45:25: 12000000 INFO @ Sun, 21 Jun 2020 19:45:26: 7000000 INFO @ Sun, 21 Jun 2020 19:45:28: 3000000 INFO @ Sun, 21 Jun 2020 19:45:32: 13000000 INFO @ Sun, 21 Jun 2020 19:45:32: 8000000 INFO @ Sun, 21 Jun 2020 19:45:34: 4000000 INFO @ Sun, 21 Jun 2020 19:45:38: 9000000 INFO @ Sun, 21 Jun 2020 19:45:38: 14000000 INFO @ Sun, 21 Jun 2020 19:45:40: 5000000 INFO @ Sun, 21 Jun 2020 19:45:44: 10000000 INFO @ Sun, 21 Jun 2020 19:45:45: 15000000 INFO @ Sun, 21 Jun 2020 19:45:46: 6000000 INFO @ Sun, 21 Jun 2020 19:45:51: 11000000 INFO @ Sun, 21 Jun 2020 19:45:51: 16000000 INFO @ Sun, 21 Jun 2020 19:45:52: 7000000 INFO @ Sun, 21 Jun 2020 19:45:57: 12000000 INFO @ Sun, 21 Jun 2020 19:45:57: 8000000 INFO @ Sun, 21 Jun 2020 19:45:58: 17000000 INFO @ Sun, 21 Jun 2020 19:46:03: 13000000 INFO @ Sun, 21 Jun 2020 19:46:03: 9000000 INFO @ Sun, 21 Jun 2020 19:46:04: 18000000 INFO @ Sun, 21 Jun 2020 19:46:09: 10000000 INFO @ Sun, 21 Jun 2020 19:46:09: 14000000 INFO @ Sun, 21 Jun 2020 19:46:11: 19000000 INFO @ Sun, 21 Jun 2020 19:46:15: 11000000 INFO @ Sun, 21 Jun 2020 19:46:16: 15000000 INFO @ Sun, 21 Jun 2020 19:46:17: 20000000 INFO @ Sun, 21 Jun 2020 19:46:21: 12000000 INFO @ Sun, 21 Jun 2020 19:46:22: 16000000 INFO @ Sun, 21 Jun 2020 19:46:23: 21000000 INFO @ Sun, 21 Jun 2020 19:46:27: 13000000 INFO @ Sun, 21 Jun 2020 19:46:29: 17000000 INFO @ Sun, 21 Jun 2020 19:46:30: 22000000 INFO @ Sun, 21 Jun 2020 19:46:33: 14000000 INFO @ Sun, 21 Jun 2020 19:46:35: 18000000 INFO @ Sun, 21 Jun 2020 19:46:37: 23000000 INFO @ Sun, 21 Jun 2020 19:46:38: 15000000 INFO @ Sun, 21 Jun 2020 19:46:41: 19000000 INFO @ Sun, 21 Jun 2020 19:46:44: 24000000 INFO @ Sun, 21 Jun 2020 19:46:44: 16000000 INFO @ Sun, 21 Jun 2020 19:46:48: 20000000 INFO @ Sun, 21 Jun 2020 19:46:50: 17000000 INFO @ Sun, 21 Jun 2020 19:46:50: 25000000 INFO @ Sun, 21 Jun 2020 19:46:54: 21000000 INFO @ Sun, 21 Jun 2020 19:46:56: 18000000 INFO @ Sun, 21 Jun 2020 19:46:57: 26000000 INFO @ Sun, 21 Jun 2020 19:47:01: 22000000 INFO @ Sun, 21 Jun 2020 19:47:02: 19000000 INFO @ Sun, 21 Jun 2020 19:47:04: 27000000 INFO @ Sun, 21 Jun 2020 19:47:05: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:47:05: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:47:05: #1 total tags in treatment: 27097875 INFO @ Sun, 21 Jun 2020 19:47:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:47:05: #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 19:47:06: #1 tags after filtering in treatment: 27097818 INFO @ Sun, 21 Jun 2020 19:47:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:47:06: #1 finished! INFO @ Sun, 21 Jun 2020 19:47:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:47:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:47:08: #2 number of paired peaks: 461 WARNING @ Sun, 21 Jun 2020 19:47:08: Fewer paired peaks (461) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 461 pairs to build model! INFO @ Sun, 21 Jun 2020 19:47:08: start model_add_line... INFO @ Sun, 21 Jun 2020 19:47:08: start X-correlation... INFO @ Sun, 21 Jun 2020 19:47:08: end of X-cor INFO @ Sun, 21 Jun 2020 19:47:08: #2 finished! INFO @ Sun, 21 Jun 2020 19:47:08: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 19:47:08: #2 alternative fragment length(s) may be 2,56 bps INFO @ Sun, 21 Jun 2020 19:47:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX306190/SRX306190.05_model.r WARNING @ Sun, 21 Jun 2020 19:47:08: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:47:08: #2 You may need to consider one of the other alternative d(s): 2,56 WARNING @ Sun, 21 Jun 2020 19:47:08: #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 19:47:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:47:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:47:08: 23000000 INFO @ Sun, 21 Jun 2020 19:47:08: 20000000 INFO @ Sun, 21 Jun 2020 19:47:14: 21000000 INFO @ Sun, 21 Jun 2020 19:47:14: 24000000 INFO @ Sun, 21 Jun 2020 19:47:20: 22000000 INFO @ Sun, 21 Jun 2020 19:47:21: 25000000 INFO @ Sun, 21 Jun 2020 19:47:26: 23000000 INFO @ Sun, 21 Jun 2020 19:47:27: 26000000 INFO @ Sun, 21 Jun 2020 19:47:32: 24000000 INFO @ Sun, 21 Jun 2020 19:47:34: 27000000 INFO @ Sun, 21 Jun 2020 19:47:35: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:47:35: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:47:35: #1 total tags in treatment: 27097875 INFO @ Sun, 21 Jun 2020 19:47:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:47:35: #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 19:47:36: #1 tags after filtering in treatment: 27097818 INFO @ Sun, 21 Jun 2020 19:47:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:47:36: #1 finished! INFO @ Sun, 21 Jun 2020 19:47:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:47:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:47:38: #2 number of paired peaks: 461 WARNING @ Sun, 21 Jun 2020 19:47:38: Fewer paired peaks (461) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 461 pairs to build model! INFO @ Sun, 21 Jun 2020 19:47:38: start model_add_line... INFO @ Sun, 21 Jun 2020 19:47:38: start X-correlation... INFO @ Sun, 21 Jun 2020 19:47:38: end of X-cor INFO @ Sun, 21 Jun 2020 19:47:38: #2 finished! INFO @ Sun, 21 Jun 2020 19:47:38: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 19:47:38: #2 alternative fragment length(s) may be 2,56 bps INFO @ Sun, 21 Jun 2020 19:47:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX306190/SRX306190.10_model.r WARNING @ Sun, 21 Jun 2020 19:47:38: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:47:38: #2 You may need to consider one of the other alternative d(s): 2,56 WARNING @ Sun, 21 Jun 2020 19:47:38: #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 19:47:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:47:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:47:38: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:47:44: 26000000 INFO @ Sun, 21 Jun 2020 19:47:50: 27000000 INFO @ Sun, 21 Jun 2020 19:47:51: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:47:51: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:47:51: #1 total tags in treatment: 27097875 INFO @ Sun, 21 Jun 2020 19:47:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:47:51: #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 19:47:52: #1 tags after filtering in treatment: 27097818 INFO @ Sun, 21 Jun 2020 19:47:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:47:52: #1 finished! INFO @ Sun, 21 Jun 2020 19:47:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:47:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:47:54: #2 number of paired peaks: 461 WARNING @ Sun, 21 Jun 2020 19:47:54: Fewer paired peaks (461) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 461 pairs to build model! INFO @ Sun, 21 Jun 2020 19:47:54: start model_add_line... INFO @ Sun, 21 Jun 2020 19:47:54: start X-correlation... INFO @ Sun, 21 Jun 2020 19:47:54: end of X-cor INFO @ Sun, 21 Jun 2020 19:47:54: #2 finished! INFO @ Sun, 21 Jun 2020 19:47:54: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 19:47:54: #2 alternative fragment length(s) may be 2,56 bps INFO @ Sun, 21 Jun 2020 19:47:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX306190/SRX306190.20_model.r WARNING @ Sun, 21 Jun 2020 19:47:54: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:47:54: #2 You may need to consider one of the other alternative d(s): 2,56 WARNING @ Sun, 21 Jun 2020 19:47:54: #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 19:47:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:47:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:48:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:48:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX306190/SRX306190.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:48:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX306190/SRX306190.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:48:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX306190/SRX306190.05_summits.bed INFO @ Sun, 21 Jun 2020 19:48:27: Done! pass1 - making usageList (765 chroms): 1 millis pass2 - checking and writing primary data (5660 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:48:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:48:49: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:48:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX306190/SRX306190.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:48:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX306190/SRX306190.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:48:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX306190/SRX306190.10_summits.bed INFO @ Sun, 21 Jun 2020 19:48:56: Done! pass1 - making usageList (602 chroms): 1 millis pass2 - checking and writing primary data (2817 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:49:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX306190/SRX306190.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:49:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX306190/SRX306190.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:49:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX306190/SRX306190.20_summits.bed INFO @ Sun, 21 Jun 2020 19:49:16: Done! pass1 - making usageList (269 chroms): 1 millis pass2 - checking and writing primary data (892 records, 4 fields): 11 millis CompletedMACS2peakCalling