Job ID = 6529963 SRX = SRX5436057 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:12:28 42102024 reads; of these: 42102024 (100.00%) were unpaired; of these: 2054494 (4.88%) aligned 0 times 28570992 (67.86%) aligned exactly 1 time 11476538 (27.26%) aligned >1 times 95.12% overall alignment rate Time searching: 00:12:28 Overall time: 00:12:28 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 20 files... [bam_rmdupse_core] 7179381 / 40047530 = 0.1793 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 @ Tue, 30 Jun 2020 03:22:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436057/SRX5436057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436057/SRX5436057.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436057/SRX5436057.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436057/SRX5436057.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 @ Tue, 30 Jun 2020 03:22:56: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:22:56: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:23:02: 1000000 INFO @ Tue, 30 Jun 2020 03:23:08: 2000000 INFO @ Tue, 30 Jun 2020 03:23:15: 3000000 INFO @ Tue, 30 Jun 2020 03:23:21: 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 @ Tue, 30 Jun 2020 03:23:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436057/SRX5436057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436057/SRX5436057.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436057/SRX5436057.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436057/SRX5436057.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 @ Tue, 30 Jun 2020 03:23:26: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:23:26: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:23:27: 5000000 INFO @ Tue, 30 Jun 2020 03:23:33: 1000000 INFO @ Tue, 30 Jun 2020 03:23:34: 6000000 INFO @ Tue, 30 Jun 2020 03:23:40: 7000000 INFO @ Tue, 30 Jun 2020 03:23:41: 2000000 INFO @ Tue, 30 Jun 2020 03:23:47: 8000000 INFO @ Tue, 30 Jun 2020 03:23:48: 3000000 INFO @ Tue, 30 Jun 2020 03:23:53: 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 @ Tue, 30 Jun 2020 03:23:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5436057/SRX5436057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5436057/SRX5436057.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5436057/SRX5436057.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5436057/SRX5436057.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 @ Tue, 30 Jun 2020 03:23:56: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:23:56: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:23:56: 4000000 INFO @ Tue, 30 Jun 2020 03:24:00: 10000000 INFO @ Tue, 30 Jun 2020 03:24:03: 1000000 INFO @ Tue, 30 Jun 2020 03:24:04: 5000000 INFO @ Tue, 30 Jun 2020 03:24:06: 11000000 INFO @ Tue, 30 Jun 2020 03:24:09: 2000000 INFO @ Tue, 30 Jun 2020 03:24:12: 6000000 INFO @ Tue, 30 Jun 2020 03:24:13: 12000000 INFO @ Tue, 30 Jun 2020 03:24:16: 3000000 INFO @ Tue, 30 Jun 2020 03:24:20: 13000000 INFO @ Tue, 30 Jun 2020 03:24:20: 7000000 INFO @ Tue, 30 Jun 2020 03:24:23: 4000000 INFO @ Tue, 30 Jun 2020 03:24:27: 14000000 INFO @ Tue, 30 Jun 2020 03:24:28: 8000000 INFO @ Tue, 30 Jun 2020 03:24:30: 5000000 INFO @ Tue, 30 Jun 2020 03:24:34: 15000000 INFO @ Tue, 30 Jun 2020 03:24:35: 9000000 INFO @ Tue, 30 Jun 2020 03:24:37: 6000000 INFO @ Tue, 30 Jun 2020 03:24:41: 16000000 INFO @ Tue, 30 Jun 2020 03:24:43: 10000000 INFO @ Tue, 30 Jun 2020 03:24:44: 7000000 INFO @ Tue, 30 Jun 2020 03:24:47: 17000000 INFO @ Tue, 30 Jun 2020 03:24:50: 11000000 INFO @ Tue, 30 Jun 2020 03:24:51: 8000000 INFO @ Tue, 30 Jun 2020 03:24:54: 18000000 INFO @ Tue, 30 Jun 2020 03:24:57: 9000000 INFO @ Tue, 30 Jun 2020 03:24:58: 12000000 INFO @ Tue, 30 Jun 2020 03:25:01: 19000000 INFO @ Tue, 30 Jun 2020 03:25:04: 10000000 INFO @ Tue, 30 Jun 2020 03:25:06: 13000000 INFO @ Tue, 30 Jun 2020 03:25:08: 20000000 INFO @ Tue, 30 Jun 2020 03:25:11: 11000000 INFO @ Tue, 30 Jun 2020 03:25:14: 14000000 INFO @ Tue, 30 Jun 2020 03:25:15: 21000000 INFO @ Tue, 30 Jun 2020 03:25:18: 12000000 INFO @ Tue, 30 Jun 2020 03:25:22: 15000000 INFO @ Tue, 30 Jun 2020 03:25:22: 22000000 INFO @ Tue, 30 Jun 2020 03:25:25: 13000000 INFO @ Tue, 30 Jun 2020 03:25:28: 23000000 INFO @ Tue, 30 Jun 2020 03:25:30: 16000000 INFO @ Tue, 30 Jun 2020 03:25:31: 14000000 INFO @ Tue, 30 Jun 2020 03:25:35: 24000000 INFO @ Tue, 30 Jun 2020 03:25:38: 17000000 INFO @ Tue, 30 Jun 2020 03:25:38: 15000000 INFO @ Tue, 30 Jun 2020 03:25:42: 25000000 INFO @ Tue, 30 Jun 2020 03:25:45: 16000000 INFO @ Tue, 30 Jun 2020 03:25:45: 18000000 INFO @ Tue, 30 Jun 2020 03:25:49: 26000000 INFO @ Tue, 30 Jun 2020 03:25:52: 17000000 INFO @ Tue, 30 Jun 2020 03:25:53: 19000000 INFO @ Tue, 30 Jun 2020 03:25:55: 27000000 INFO @ Tue, 30 Jun 2020 03:25:59: 18000000 INFO @ Tue, 30 Jun 2020 03:26:01: 20000000 INFO @ Tue, 30 Jun 2020 03:26:03: 28000000 INFO @ Tue, 30 Jun 2020 03:26:06: 19000000 INFO @ Tue, 30 Jun 2020 03:26:09: 21000000 INFO @ Tue, 30 Jun 2020 03:26:10: 29000000 INFO @ Tue, 30 Jun 2020 03:26:13: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:26:16: 30000000 INFO @ Tue, 30 Jun 2020 03:26:17: 22000000 INFO @ Tue, 30 Jun 2020 03:26:20: 21000000 INFO @ Tue, 30 Jun 2020 03:26:23: 31000000 INFO @ Tue, 30 Jun 2020 03:26:25: 23000000 INFO @ Tue, 30 Jun 2020 03:26:27: 22000000 INFO @ Tue, 30 Jun 2020 03:26:30: 32000000 INFO @ Tue, 30 Jun 2020 03:26:33: 24000000 INFO @ Tue, 30 Jun 2020 03:26:34: 23000000 INFO @ Tue, 30 Jun 2020 03:26:36: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:26:36: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:26:36: #1 total tags in treatment: 32868149 INFO @ Tue, 30 Jun 2020 03:26:36: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:26:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:26:37: #1 tags after filtering in treatment: 32868112 INFO @ Tue, 30 Jun 2020 03:26:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:26:37: #1 finished! INFO @ Tue, 30 Jun 2020 03:26:37: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:26:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:26:39: #2 number of paired peaks: 358 WARNING @ Tue, 30 Jun 2020 03:26:39: 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 @ Tue, 30 Jun 2020 03:26:39: start model_add_line... INFO @ Tue, 30 Jun 2020 03:26:40: start X-correlation... INFO @ Tue, 30 Jun 2020 03:26:40: end of X-cor INFO @ Tue, 30 Jun 2020 03:26:40: #2 finished! INFO @ Tue, 30 Jun 2020 03:26:40: #2 predicted fragment length is 52 bps INFO @ Tue, 30 Jun 2020 03:26:40: #2 alternative fragment length(s) may be 1,52 bps INFO @ Tue, 30 Jun 2020 03:26:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436057/SRX5436057.05_model.r WARNING @ Tue, 30 Jun 2020 03:26:40: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:26:40: #2 You may need to consider one of the other alternative d(s): 1,52 WARNING @ Tue, 30 Jun 2020 03:26:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:26:40: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:26:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:26:40: 24000000 INFO @ Tue, 30 Jun 2020 03:26:41: 25000000 INFO @ Tue, 30 Jun 2020 03:26:47: 25000000 INFO @ Tue, 30 Jun 2020 03:26:49: 26000000 INFO @ Tue, 30 Jun 2020 03:26:54: 26000000 INFO @ Tue, 30 Jun 2020 03:26:57: 27000000 INFO @ Tue, 30 Jun 2020 03:27:00: 27000000 INFO @ Tue, 30 Jun 2020 03:27:05: 28000000 INFO @ Tue, 30 Jun 2020 03:27:07: 28000000 INFO @ Tue, 30 Jun 2020 03:27:12: 29000000 INFO @ Tue, 30 Jun 2020 03:27:14: 29000000 INFO @ Tue, 30 Jun 2020 03:27:19: 30000000 INFO @ Tue, 30 Jun 2020 03:27:20: 30000000 INFO @ Tue, 30 Jun 2020 03:27:26: 31000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:27:27: 31000000 INFO @ Tue, 30 Jun 2020 03:27:33: 32000000 INFO @ Tue, 30 Jun 2020 03:27:34: 32000000 INFO @ Tue, 30 Jun 2020 03:27:39: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:27:39: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:27:39: #1 total tags in treatment: 32868149 INFO @ Tue, 30 Jun 2020 03:27:39: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:27:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:27:40: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:27:40: #1 tags after filtering in treatment: 32868112 INFO @ Tue, 30 Jun 2020 03:27:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:27:40: #1 finished! INFO @ Tue, 30 Jun 2020 03:27:40: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:27:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:27:40: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:27:40: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:27:40: #1 total tags in treatment: 32868149 INFO @ Tue, 30 Jun 2020 03:27:40: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:27:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:27:41: #1 tags after filtering in treatment: 32868112 INFO @ Tue, 30 Jun 2020 03:27:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:27:41: #1 finished! INFO @ Tue, 30 Jun 2020 03:27:41: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:27:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:27:42: #2 number of paired peaks: 358 WARNING @ Tue, 30 Jun 2020 03:27:42: 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 @ Tue, 30 Jun 2020 03:27:42: start model_add_line... INFO @ Tue, 30 Jun 2020 03:27:42: start X-correlation... INFO @ Tue, 30 Jun 2020 03:27:42: end of X-cor INFO @ Tue, 30 Jun 2020 03:27:42: #2 finished! INFO @ Tue, 30 Jun 2020 03:27:42: #2 predicted fragment length is 52 bps INFO @ Tue, 30 Jun 2020 03:27:42: #2 alternative fragment length(s) may be 1,52 bps INFO @ Tue, 30 Jun 2020 03:27:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436057/SRX5436057.10_model.r WARNING @ Tue, 30 Jun 2020 03:27:42: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:27:42: #2 You may need to consider one of the other alternative d(s): 1,52 WARNING @ Tue, 30 Jun 2020 03:27:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:27:42: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:27:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:27:43: #2 number of paired peaks: 358 WARNING @ Tue, 30 Jun 2020 03:27:43: 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 @ Tue, 30 Jun 2020 03:27:43: start model_add_line... INFO @ Tue, 30 Jun 2020 03:27:43: start X-correlation... INFO @ Tue, 30 Jun 2020 03:27:43: end of X-cor INFO @ Tue, 30 Jun 2020 03:27:43: #2 finished! INFO @ Tue, 30 Jun 2020 03:27:43: #2 predicted fragment length is 52 bps INFO @ Tue, 30 Jun 2020 03:27:43: #2 alternative fragment length(s) may be 1,52 bps INFO @ Tue, 30 Jun 2020 03:27:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5436057/SRX5436057.20_model.r WARNING @ Tue, 30 Jun 2020 03:27:43: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:27:43: #2 You may need to consider one of the other alternative d(s): 1,52 WARNING @ Tue, 30 Jun 2020 03:27:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:27:43: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:27:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:28:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436057/SRX5436057.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:28:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436057/SRX5436057.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:28:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436057/SRX5436057.05_summits.bed INFO @ Tue, 30 Jun 2020 03:28:08: Done! pass1 - making usageList (669 chroms): 1 millis pass2 - checking and writing primary data (4258 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:28:39: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:28:42: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:29:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436057/SRX5436057.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:29:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436057/SRX5436057.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:29:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436057/SRX5436057.10_summits.bed INFO @ Tue, 30 Jun 2020 03:29:05: Done! pass1 - making usageList (523 chroms): 1 millis pass2 - checking and writing primary data (2356 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:29:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5436057/SRX5436057.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:29:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5436057/SRX5436057.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:29:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5436057/SRX5436057.20_summits.bed INFO @ Tue, 30 Jun 2020 03:29:11: Done! pass1 - making usageList (403 chroms): 1 millis pass2 - checking and writing primary data (1406 records, 4 fields): 12 millis CompletedMACS2peakCalling