Job ID = 6529697 SRX = SRX3981678 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: 00:10:34 39112330 reads; of these: 39112330 (100.00%) were unpaired; of these: 1291100 (3.30%) aligned 0 times 27786908 (71.04%) aligned exactly 1 time 10034322 (25.66%) aligned >1 times 96.70% overall alignment rate Time searching: 00:10:34 Overall time: 00:10:34 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] 5174795 / 37821230 = 0.1368 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 02:53:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981678/SRX3981678.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981678/SRX3981678.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981678/SRX3981678.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981678/SRX3981678.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 02:53:30: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:53:30: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:53:36: 1000000 INFO @ Tue, 30 Jun 2020 02:53:41: 2000000 INFO @ Tue, 30 Jun 2020 02:53:46: 3000000 INFO @ Tue, 30 Jun 2020 02:53:52: 4000000 INFO @ Tue, 30 Jun 2020 02:53:57: 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 02:54:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981678/SRX3981678.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981678/SRX3981678.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981678/SRX3981678.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981678/SRX3981678.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 02:54:01: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:54:01: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:54:03: 6000000 INFO @ Tue, 30 Jun 2020 02:54:06: 1000000 INFO @ Tue, 30 Jun 2020 02:54:08: 7000000 INFO @ Tue, 30 Jun 2020 02:54:12: 2000000 INFO @ Tue, 30 Jun 2020 02:54:14: 8000000 INFO @ Tue, 30 Jun 2020 02:54:18: 3000000 INFO @ Tue, 30 Jun 2020 02:54:20: 9000000 INFO @ Tue, 30 Jun 2020 02:54:23: 4000000 INFO @ Tue, 30 Jun 2020 02:54:25: 10000000 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 02:54:29: 5000000 INFO @ Tue, 30 Jun 2020 02:54:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981678/SRX3981678.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981678/SRX3981678.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981678/SRX3981678.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981678/SRX3981678.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 02:54:30: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:54:30: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:54:31: 11000000 INFO @ Tue, 30 Jun 2020 02:54:35: 6000000 INFO @ Tue, 30 Jun 2020 02:54:36: 1000000 INFO @ Tue, 30 Jun 2020 02:54:37: 12000000 INFO @ Tue, 30 Jun 2020 02:54:40: 7000000 INFO @ Tue, 30 Jun 2020 02:54:42: 2000000 INFO @ Tue, 30 Jun 2020 02:54:43: 13000000 INFO @ Tue, 30 Jun 2020 02:54:46: 8000000 INFO @ Tue, 30 Jun 2020 02:54:48: 3000000 INFO @ Tue, 30 Jun 2020 02:54:48: 14000000 INFO @ Tue, 30 Jun 2020 02:54:52: 9000000 INFO @ Tue, 30 Jun 2020 02:54:53: 4000000 INFO @ Tue, 30 Jun 2020 02:54:54: 15000000 INFO @ Tue, 30 Jun 2020 02:54:58: 10000000 INFO @ Tue, 30 Jun 2020 02:54:59: 5000000 INFO @ Tue, 30 Jun 2020 02:55:00: 16000000 INFO @ Tue, 30 Jun 2020 02:55:03: 11000000 INFO @ Tue, 30 Jun 2020 02:55:05: 6000000 INFO @ Tue, 30 Jun 2020 02:55:06: 17000000 INFO @ Tue, 30 Jun 2020 02:55:09: 12000000 INFO @ Tue, 30 Jun 2020 02:55:10: 7000000 INFO @ Tue, 30 Jun 2020 02:55:11: 18000000 INFO @ Tue, 30 Jun 2020 02:55:15: 13000000 INFO @ Tue, 30 Jun 2020 02:55:16: 8000000 INFO @ Tue, 30 Jun 2020 02:55:17: 19000000 INFO @ Tue, 30 Jun 2020 02:55:21: 14000000 INFO @ Tue, 30 Jun 2020 02:55:22: 9000000 INFO @ Tue, 30 Jun 2020 02:55:22: 20000000 INFO @ Tue, 30 Jun 2020 02:55:26: 15000000 INFO @ Tue, 30 Jun 2020 02:55:27: 10000000 INFO @ Tue, 30 Jun 2020 02:55:28: 21000000 INFO @ Tue, 30 Jun 2020 02:55:32: 16000000 INFO @ Tue, 30 Jun 2020 02:55:33: 11000000 INFO @ Tue, 30 Jun 2020 02:55:33: 22000000 INFO @ Tue, 30 Jun 2020 02:55:37: 17000000 INFO @ Tue, 30 Jun 2020 02:55:39: 12000000 INFO @ Tue, 30 Jun 2020 02:55:39: 23000000 INFO @ Tue, 30 Jun 2020 02:55:43: 18000000 INFO @ Tue, 30 Jun 2020 02:55:44: 13000000 INFO @ Tue, 30 Jun 2020 02:55:44: 24000000 INFO @ Tue, 30 Jun 2020 02:55:49: 19000000 INFO @ Tue, 30 Jun 2020 02:55:50: 14000000 INFO @ Tue, 30 Jun 2020 02:55:50: 25000000 INFO @ Tue, 30 Jun 2020 02:55:54: 20000000 INFO @ Tue, 30 Jun 2020 02:55:55: 26000000 INFO @ Tue, 30 Jun 2020 02:55:55: 15000000 INFO @ Tue, 30 Jun 2020 02:56:00: 21000000 INFO @ Tue, 30 Jun 2020 02:56:01: 27000000 INFO @ Tue, 30 Jun 2020 02:56:01: 16000000 INFO @ Tue, 30 Jun 2020 02:56:05: 22000000 INFO @ Tue, 30 Jun 2020 02:56:06: 17000000 INFO @ Tue, 30 Jun 2020 02:56:06: 28000000 INFO @ Tue, 30 Jun 2020 02:56:10: 23000000 INFO @ Tue, 30 Jun 2020 02:56:12: 18000000 INFO @ Tue, 30 Jun 2020 02:56:12: 29000000 INFO @ Tue, 30 Jun 2020 02:56:16: 24000000 INFO @ Tue, 30 Jun 2020 02:56:17: 19000000 INFO @ Tue, 30 Jun 2020 02:56:17: 30000000 INFO @ Tue, 30 Jun 2020 02:56:21: 25000000 INFO @ Tue, 30 Jun 2020 02:56:23: 20000000 INFO @ Tue, 30 Jun 2020 02:56:23: 31000000 INFO @ Tue, 30 Jun 2020 02:56:27: 26000000 INFO @ Tue, 30 Jun 2020 02:56:28: 21000000 INFO @ Tue, 30 Jun 2020 02:56:29: 32000000 INFO @ Tue, 30 Jun 2020 02:56:32: 27000000 INFO @ Tue, 30 Jun 2020 02:56:33: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:56:33: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:56:33: #1 total tags in treatment: 32646435 INFO @ Tue, 30 Jun 2020 02:56:33: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:56:33: #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 02:56:33: #1 tags after filtering in treatment: 32646396 INFO @ Tue, 30 Jun 2020 02:56:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:56:33: #1 finished! INFO @ Tue, 30 Jun 2020 02:56:33: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:56:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:56:33: 22000000 INFO @ Tue, 30 Jun 2020 02:56:35: #2 number of paired peaks: 185 WARNING @ Tue, 30 Jun 2020 02:56:35: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Tue, 30 Jun 2020 02:56:35: start model_add_line... INFO @ Tue, 30 Jun 2020 02:56:35: start X-correlation... INFO @ Tue, 30 Jun 2020 02:56:35: end of X-cor INFO @ Tue, 30 Jun 2020 02:56:35: #2 finished! INFO @ Tue, 30 Jun 2020 02:56:35: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 02:56:35: #2 alternative fragment length(s) may be 1,50,588 bps INFO @ Tue, 30 Jun 2020 02:56:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981678/SRX3981678.05_model.r WARNING @ Tue, 30 Jun 2020 02:56:35: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:56:35: #2 You may need to consider one of the other alternative d(s): 1,50,588 WARNING @ Tue, 30 Jun 2020 02:56:35: #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 02:56:35: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:56:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:56:38: 28000000 INFO @ Tue, 30 Jun 2020 02:56:39: 23000000 INFO @ Tue, 30 Jun 2020 02:56:44: 29000000 INFO @ Tue, 30 Jun 2020 02:56:44: 24000000 INFO @ Tue, 30 Jun 2020 02:56:49: 30000000 INFO @ Tue, 30 Jun 2020 02:56:50: 25000000 INFO @ Tue, 30 Jun 2020 02:56:55: 31000000 INFO @ Tue, 30 Jun 2020 02:56:55: 26000000 INFO @ Tue, 30 Jun 2020 02:57:00: 32000000 INFO @ Tue, 30 Jun 2020 02:57:00: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:57:04: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:57:04: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:57:04: #1 total tags in treatment: 32646435 INFO @ Tue, 30 Jun 2020 02:57:04: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:57:04: #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 02:57:05: #1 tags after filtering in treatment: 32646396 INFO @ Tue, 30 Jun 2020 02:57:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:57:05: #1 finished! INFO @ Tue, 30 Jun 2020 02:57:05: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:57:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:57:06: 28000000 INFO @ Tue, 30 Jun 2020 02:57:07: #2 number of paired peaks: 185 WARNING @ Tue, 30 Jun 2020 02:57:07: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Tue, 30 Jun 2020 02:57:07: start model_add_line... INFO @ Tue, 30 Jun 2020 02:57:07: start X-correlation... INFO @ Tue, 30 Jun 2020 02:57:07: end of X-cor INFO @ Tue, 30 Jun 2020 02:57:07: #2 finished! INFO @ Tue, 30 Jun 2020 02:57:07: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 02:57:07: #2 alternative fragment length(s) may be 1,50,588 bps INFO @ Tue, 30 Jun 2020 02:57:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981678/SRX3981678.10_model.r WARNING @ Tue, 30 Jun 2020 02:57:07: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:57:07: #2 You may need to consider one of the other alternative d(s): 1,50,588 WARNING @ Tue, 30 Jun 2020 02:57:07: #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 02:57:07: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:57:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:57:11: 29000000 INFO @ Tue, 30 Jun 2020 02:57:17: 30000000 INFO @ Tue, 30 Jun 2020 02:57:22: 31000000 INFO @ Tue, 30 Jun 2020 02:57:26: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:57:27: 32000000 INFO @ Tue, 30 Jun 2020 02:57:31: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:57:31: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:57:31: #1 total tags in treatment: 32646435 INFO @ Tue, 30 Jun 2020 02:57:31: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:57:31: #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 02:57:32: #1 tags after filtering in treatment: 32646396 INFO @ Tue, 30 Jun 2020 02:57:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:57:32: #1 finished! INFO @ Tue, 30 Jun 2020 02:57:32: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:57:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:57:34: #2 number of paired peaks: 185 WARNING @ Tue, 30 Jun 2020 02:57:34: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Tue, 30 Jun 2020 02:57:34: start model_add_line... INFO @ Tue, 30 Jun 2020 02:57:34: start X-correlation... INFO @ Tue, 30 Jun 2020 02:57:34: end of X-cor INFO @ Tue, 30 Jun 2020 02:57:34: #2 finished! INFO @ Tue, 30 Jun 2020 02:57:34: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 02:57:34: #2 alternative fragment length(s) may be 1,50,588 bps INFO @ Tue, 30 Jun 2020 02:57:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981678/SRX3981678.20_model.r WARNING @ Tue, 30 Jun 2020 02:57:34: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:57:34: #2 You may need to consider one of the other alternative d(s): 1,50,588 WARNING @ Tue, 30 Jun 2020 02:57:34: #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 02:57:34: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:57:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:57:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981678/SRX3981678.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:57:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981678/SRX3981678.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:57:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981678/SRX3981678.05_summits.bed INFO @ Tue, 30 Jun 2020 02:57:50: Done! pass1 - making usageList (633 chroms): 1 millis pass2 - checking and writing primary data (3070 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:57:57: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:58:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981678/SRX3981678.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:58:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981678/SRX3981678.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:58:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981678/SRX3981678.10_summits.bed INFO @ Tue, 30 Jun 2020 02:58:22: Done! pass1 - making usageList (502 chroms): 1 millis pass2 - checking and writing primary data (2086 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:58:26: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:58:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981678/SRX3981678.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:58:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981678/SRX3981678.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:58:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981678/SRX3981678.20_summits.bed INFO @ Tue, 30 Jun 2020 02:58:51: Done! pass1 - making usageList (304 chroms): 1 millis pass2 - checking and writing primary data (721 records, 4 fields): 9 millis CompletedMACS2peakCalling