Job ID = 6529300 SRX = SRX1433359 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: 00:11:16 44281887 reads; of these: 44281887 (100.00%) were unpaired; of these: 1310727 (2.96%) aligned 0 times 34249545 (77.34%) aligned exactly 1 time 8721615 (19.70%) aligned >1 times 97.04% overall alignment rate Time searching: 00:11:16 Overall time: 00:11:16 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 20 files... [bam_rmdupse_core] 13982012 / 42971160 = 0.3254 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 02:45:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433359/SRX1433359.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433359/SRX1433359.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433359/SRX1433359.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433359/SRX1433359.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 02:45:09: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:45:09: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:45:14: 1000000 INFO @ Tue, 30 Jun 2020 02:45:19: 2000000 INFO @ Tue, 30 Jun 2020 02:45:24: 3000000 INFO @ Tue, 30 Jun 2020 02:45:29: 4000000 INFO @ Tue, 30 Jun 2020 02:45:34: 5000000 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 02:45:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433359/SRX1433359.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433359/SRX1433359.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433359/SRX1433359.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433359/SRX1433359.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 02:45:39: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:45:39: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:45:39: 6000000 INFO @ Tue, 30 Jun 2020 02:45:44: 1000000 INFO @ Tue, 30 Jun 2020 02:45:44: 7000000 INFO @ Tue, 30 Jun 2020 02:45:49: 2000000 INFO @ Tue, 30 Jun 2020 02:45:49: 8000000 INFO @ Tue, 30 Jun 2020 02:45:54: 3000000 INFO @ Tue, 30 Jun 2020 02:45:54: 9000000 INFO @ Tue, 30 Jun 2020 02:45:59: 4000000 INFO @ Tue, 30 Jun 2020 02:46:00: 10000000 INFO @ Tue, 30 Jun 2020 02:46:05: 5000000 INFO @ Tue, 30 Jun 2020 02:46:05: 11000000 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 02:46:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433359/SRX1433359.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433359/SRX1433359.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433359/SRX1433359.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433359/SRX1433359.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 02:46:09: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:46:09: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:46:10: 6000000 INFO @ Tue, 30 Jun 2020 02:46:10: 12000000 INFO @ Tue, 30 Jun 2020 02:46:14: 1000000 INFO @ Tue, 30 Jun 2020 02:46:16: 7000000 INFO @ Tue, 30 Jun 2020 02:46:16: 13000000 INFO @ Tue, 30 Jun 2020 02:46:20: 2000000 INFO @ Tue, 30 Jun 2020 02:46:22: 8000000 INFO @ Tue, 30 Jun 2020 02:46:22: 14000000 INFO @ Tue, 30 Jun 2020 02:46:26: 3000000 INFO @ Tue, 30 Jun 2020 02:46:27: 9000000 INFO @ Tue, 30 Jun 2020 02:46:28: 15000000 INFO @ Tue, 30 Jun 2020 02:46:32: 4000000 INFO @ Tue, 30 Jun 2020 02:46:33: 10000000 INFO @ Tue, 30 Jun 2020 02:46:33: 16000000 INFO @ Tue, 30 Jun 2020 02:46:38: 5000000 INFO @ Tue, 30 Jun 2020 02:46:39: 11000000 INFO @ Tue, 30 Jun 2020 02:46:39: 17000000 INFO @ Tue, 30 Jun 2020 02:46:43: 6000000 INFO @ Tue, 30 Jun 2020 02:46:45: 12000000 INFO @ Tue, 30 Jun 2020 02:46:45: 18000000 INFO @ Tue, 30 Jun 2020 02:46:49: 7000000 INFO @ Tue, 30 Jun 2020 02:46:50: 13000000 INFO @ Tue, 30 Jun 2020 02:46:51: 19000000 INFO @ Tue, 30 Jun 2020 02:46:55: 8000000 INFO @ Tue, 30 Jun 2020 02:46:56: 14000000 INFO @ Tue, 30 Jun 2020 02:46:56: 20000000 INFO @ Tue, 30 Jun 2020 02:47:00: 9000000 INFO @ Tue, 30 Jun 2020 02:47:02: 15000000 INFO @ Tue, 30 Jun 2020 02:47:02: 21000000 INFO @ Tue, 30 Jun 2020 02:47:06: 10000000 INFO @ Tue, 30 Jun 2020 02:47:07: 16000000 INFO @ Tue, 30 Jun 2020 02:47:08: 22000000 INFO @ Tue, 30 Jun 2020 02:47:12: 11000000 INFO @ Tue, 30 Jun 2020 02:47:13: 17000000 INFO @ Tue, 30 Jun 2020 02:47:13: 23000000 INFO @ Tue, 30 Jun 2020 02:47:17: 12000000 INFO @ Tue, 30 Jun 2020 02:47:19: 18000000 INFO @ Tue, 30 Jun 2020 02:47:19: 24000000 INFO @ Tue, 30 Jun 2020 02:47:23: 13000000 INFO @ Tue, 30 Jun 2020 02:47:24: 19000000 INFO @ Tue, 30 Jun 2020 02:47:25: 25000000 INFO @ Tue, 30 Jun 2020 02:47:28: 14000000 INFO @ Tue, 30 Jun 2020 02:47:30: 20000000 INFO @ Tue, 30 Jun 2020 02:47:31: 26000000 INFO @ Tue, 30 Jun 2020 02:47:34: 15000000 INFO @ Tue, 30 Jun 2020 02:47:35: 21000000 INFO @ Tue, 30 Jun 2020 02:47:36: 27000000 INFO @ Tue, 30 Jun 2020 02:47:40: 16000000 INFO @ Tue, 30 Jun 2020 02:47:41: 22000000 INFO @ Tue, 30 Jun 2020 02:47:42: 28000000 INFO @ Tue, 30 Jun 2020 02:47:45: 17000000 INFO @ Tue, 30 Jun 2020 02:47:47: 23000000 INFO @ Tue, 30 Jun 2020 02:47:48: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:47:48: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:47:48: #1 total tags in treatment: 28989148 INFO @ Tue, 30 Jun 2020 02:47:48: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:47:48: #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 02:47:49: #1 tags after filtering in treatment: 28989102 INFO @ Tue, 30 Jun 2020 02:47:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:47:49: #1 finished! INFO @ Tue, 30 Jun 2020 02:47:49: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:47:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:47:51: #2 number of paired peaks: 194 WARNING @ Tue, 30 Jun 2020 02:47:51: Fewer paired peaks (194) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 194 pairs to build model! INFO @ Tue, 30 Jun 2020 02:47:51: start model_add_line... INFO @ Tue, 30 Jun 2020 02:47:51: start X-correlation... INFO @ Tue, 30 Jun 2020 02:47:51: end of X-cor INFO @ Tue, 30 Jun 2020 02:47:51: #2 finished! INFO @ Tue, 30 Jun 2020 02:47:51: #2 predicted fragment length is 65 bps INFO @ Tue, 30 Jun 2020 02:47:51: #2 alternative fragment length(s) may be 2,47,65 bps INFO @ Tue, 30 Jun 2020 02:47:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433359/SRX1433359.05_model.r WARNING @ Tue, 30 Jun 2020 02:47:51: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:47:51: #2 You may need to consider one of the other alternative d(s): 2,47,65 WARNING @ Tue, 30 Jun 2020 02:47:51: #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 02:47:51: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:47:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:47:51: 18000000 INFO @ Tue, 30 Jun 2020 02:47:53: 24000000 INFO @ Tue, 30 Jun 2020 02:47:57: 19000000 INFO @ Tue, 30 Jun 2020 02:47:58: 25000000 INFO @ Tue, 30 Jun 2020 02:48:02: 20000000 INFO @ Tue, 30 Jun 2020 02:48:04: 26000000 INFO @ Tue, 30 Jun 2020 02:48:08: 21000000 INFO @ Tue, 30 Jun 2020 02:48:09: 27000000 INFO @ Tue, 30 Jun 2020 02:48:13: 22000000 INFO @ Tue, 30 Jun 2020 02:48:15: 28000000 INFO @ Tue, 30 Jun 2020 02:48:19: 23000000 INFO @ Tue, 30 Jun 2020 02:48:21: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:48:21: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:48:21: #1 total tags in treatment: 28989148 INFO @ Tue, 30 Jun 2020 02:48:21: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:48:21: #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 02:48:22: #1 tags after filtering in treatment: 28989102 INFO @ Tue, 30 Jun 2020 02:48:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:48:22: #1 finished! INFO @ Tue, 30 Jun 2020 02:48:22: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:48:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:48:24: #2 number of paired peaks: 194 WARNING @ Tue, 30 Jun 2020 02:48:24: Fewer paired peaks (194) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 194 pairs to build model! INFO @ Tue, 30 Jun 2020 02:48:24: start model_add_line... INFO @ Tue, 30 Jun 2020 02:48:24: start X-correlation... INFO @ Tue, 30 Jun 2020 02:48:24: end of X-cor INFO @ Tue, 30 Jun 2020 02:48:24: #2 finished! INFO @ Tue, 30 Jun 2020 02:48:24: #2 predicted fragment length is 65 bps INFO @ Tue, 30 Jun 2020 02:48:24: #2 alternative fragment length(s) may be 2,47,65 bps INFO @ Tue, 30 Jun 2020 02:48:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433359/SRX1433359.10_model.r WARNING @ Tue, 30 Jun 2020 02:48:24: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:48:24: #2 You may need to consider one of the other alternative d(s): 2,47,65 WARNING @ Tue, 30 Jun 2020 02:48:24: #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 02:48:24: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:48:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:48:25: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:48:30: 25000000 INFO @ Tue, 30 Jun 2020 02:48:35: 26000000 INFO @ Tue, 30 Jun 2020 02:48:40: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:48:41: 27000000 INFO @ Tue, 30 Jun 2020 02:48:46: 28000000 INFO @ Tue, 30 Jun 2020 02:48:52: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:48:52: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:48:52: #1 total tags in treatment: 28989148 INFO @ Tue, 30 Jun 2020 02:48:52: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:48:52: #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 02:48:53: #1 tags after filtering in treatment: 28989102 INFO @ Tue, 30 Jun 2020 02:48:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:48:53: #1 finished! INFO @ Tue, 30 Jun 2020 02:48:53: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:48:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:48:54: #2 number of paired peaks: 194 WARNING @ Tue, 30 Jun 2020 02:48:54: Fewer paired peaks (194) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 194 pairs to build model! INFO @ Tue, 30 Jun 2020 02:48:54: start model_add_line... INFO @ Tue, 30 Jun 2020 02:48:55: start X-correlation... INFO @ Tue, 30 Jun 2020 02:48:55: end of X-cor INFO @ Tue, 30 Jun 2020 02:48:55: #2 finished! INFO @ Tue, 30 Jun 2020 02:48:55: #2 predicted fragment length is 65 bps INFO @ Tue, 30 Jun 2020 02:48:55: #2 alternative fragment length(s) may be 2,47,65 bps INFO @ Tue, 30 Jun 2020 02:48:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433359/SRX1433359.20_model.r WARNING @ Tue, 30 Jun 2020 02:48:55: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:48:55: #2 You may need to consider one of the other alternative d(s): 2,47,65 WARNING @ Tue, 30 Jun 2020 02:48:55: #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 02:48:55: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:48:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:49:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433359/SRX1433359.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:49:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433359/SRX1433359.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:49:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433359/SRX1433359.05_summits.bed INFO @ Tue, 30 Jun 2020 02:49:06: Done! pass1 - making usageList (580 chroms): 1 millis pass2 - checking and writing primary data (2668 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:49:12: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:49:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433359/SRX1433359.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:49:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433359/SRX1433359.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:49:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433359/SRX1433359.10_summits.bed INFO @ Tue, 30 Jun 2020 02:49:36: Done! pass1 - making usageList (380 chroms): 1 millis pass2 - checking and writing primary data (1146 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:49:44: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:50:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433359/SRX1433359.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:50:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433359/SRX1433359.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:50:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433359/SRX1433359.20_summits.bed INFO @ Tue, 30 Jun 2020 02:50:08: Done! pass1 - making usageList (133 chroms): 1 millis pass2 - checking and writing primary data (317 records, 4 fields): 5 millis CompletedMACS2peakCalling