Job ID = 6529354 SRX = SRX201888 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: 00:27:15 51149396 reads; of these: 51149396 (100.00%) were unpaired; of these: 1268692 (2.48%) aligned 0 times 36935788 (72.21%) aligned exactly 1 time 12944916 (25.31%) aligned >1 times 97.52% overall alignment rate Time searching: 00:27:15 Overall time: 00:27:15 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 24 files... [bam_rmdupse_core] 12020955 / 49880704 = 0.2410 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 02:36:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX201888/SRX201888.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX201888/SRX201888.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX201888/SRX201888.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX201888/SRX201888.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 02:36:03: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:36:03: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:36:11: 1000000 INFO @ Tue, 30 Jun 2020 02:36:19: 2000000 INFO @ Tue, 30 Jun 2020 02:36:27: 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 @ Tue, 30 Jun 2020 02:36:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX201888/SRX201888.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX201888/SRX201888.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX201888/SRX201888.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX201888/SRX201888.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 02:36:33: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:36:33: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:36:35: 4000000 INFO @ Tue, 30 Jun 2020 02:36:41: 1000000 INFO @ Tue, 30 Jun 2020 02:36:43: 5000000 INFO @ Tue, 30 Jun 2020 02:36:50: 2000000 INFO @ Tue, 30 Jun 2020 02:36:52: 6000000 INFO @ Tue, 30 Jun 2020 02:36:58: 3000000 INFO @ Tue, 30 Jun 2020 02:37:00: 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 @ Tue, 30 Jun 2020 02:37:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX201888/SRX201888.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX201888/SRX201888.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX201888/SRX201888.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX201888/SRX201888.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 02:37:03: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:37:03: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:37:07: 4000000 INFO @ Tue, 30 Jun 2020 02:37:09: 8000000 INFO @ Tue, 30 Jun 2020 02:37:11: 1000000 INFO @ Tue, 30 Jun 2020 02:37:15: 5000000 INFO @ Tue, 30 Jun 2020 02:37:18: 9000000 INFO @ Tue, 30 Jun 2020 02:37:18: 2000000 INFO @ Tue, 30 Jun 2020 02:37:24: 6000000 INFO @ Tue, 30 Jun 2020 02:37:25: 3000000 INFO @ Tue, 30 Jun 2020 02:37:27: 10000000 INFO @ Tue, 30 Jun 2020 02:37:32: 4000000 INFO @ Tue, 30 Jun 2020 02:37:33: 7000000 INFO @ Tue, 30 Jun 2020 02:37:35: 11000000 INFO @ Tue, 30 Jun 2020 02:37:39: 5000000 INFO @ Tue, 30 Jun 2020 02:37:41: 8000000 INFO @ Tue, 30 Jun 2020 02:37:44: 12000000 INFO @ Tue, 30 Jun 2020 02:37:46: 6000000 INFO @ Tue, 30 Jun 2020 02:37:49: 9000000 INFO @ Tue, 30 Jun 2020 02:37:52: 13000000 INFO @ Tue, 30 Jun 2020 02:37:53: 7000000 INFO @ Tue, 30 Jun 2020 02:37:57: 10000000 INFO @ Tue, 30 Jun 2020 02:38:00: 8000000 INFO @ Tue, 30 Jun 2020 02:38:00: 14000000 INFO @ Tue, 30 Jun 2020 02:38:05: 11000000 INFO @ Tue, 30 Jun 2020 02:38:07: 9000000 INFO @ Tue, 30 Jun 2020 02:38:09: 15000000 INFO @ Tue, 30 Jun 2020 02:38:14: 12000000 INFO @ Tue, 30 Jun 2020 02:38:14: 10000000 INFO @ Tue, 30 Jun 2020 02:38:17: 16000000 INFO @ Tue, 30 Jun 2020 02:38:21: 11000000 INFO @ Tue, 30 Jun 2020 02:38:22: 13000000 INFO @ Tue, 30 Jun 2020 02:38:25: 17000000 INFO @ Tue, 30 Jun 2020 02:38:28: 12000000 INFO @ Tue, 30 Jun 2020 02:38:30: 14000000 INFO @ Tue, 30 Jun 2020 02:38:33: 18000000 INFO @ Tue, 30 Jun 2020 02:38:34: 13000000 INFO @ Tue, 30 Jun 2020 02:38:38: 15000000 INFO @ Tue, 30 Jun 2020 02:38:41: 19000000 INFO @ Tue, 30 Jun 2020 02:38:41: 14000000 INFO @ Tue, 30 Jun 2020 02:38:45: 16000000 INFO @ Tue, 30 Jun 2020 02:38:48: 15000000 INFO @ Tue, 30 Jun 2020 02:38:49: 20000000 INFO @ Tue, 30 Jun 2020 02:38:53: 17000000 INFO @ Tue, 30 Jun 2020 02:38:55: 16000000 INFO @ Tue, 30 Jun 2020 02:38:57: 21000000 INFO @ Tue, 30 Jun 2020 02:39:01: 18000000 INFO @ Tue, 30 Jun 2020 02:39:02: 17000000 INFO @ Tue, 30 Jun 2020 02:39:05: 22000000 INFO @ Tue, 30 Jun 2020 02:39:09: 18000000 INFO @ Tue, 30 Jun 2020 02:39:09: 19000000 INFO @ Tue, 30 Jun 2020 02:39:13: 23000000 INFO @ Tue, 30 Jun 2020 02:39:16: 19000000 INFO @ Tue, 30 Jun 2020 02:39:17: 20000000 INFO @ Tue, 30 Jun 2020 02:39:21: 24000000 INFO @ Tue, 30 Jun 2020 02:39:23: 20000000 INFO @ Tue, 30 Jun 2020 02:39:25: 21000000 INFO @ Tue, 30 Jun 2020 02:39:29: 25000000 INFO @ Tue, 30 Jun 2020 02:39:30: 21000000 INFO @ Tue, 30 Jun 2020 02:39:33: 22000000 INFO @ Tue, 30 Jun 2020 02:39:36: 22000000 INFO @ Tue, 30 Jun 2020 02:39:37: 26000000 INFO @ Tue, 30 Jun 2020 02:39:41: 23000000 INFO @ Tue, 30 Jun 2020 02:39:43: 23000000 INFO @ Tue, 30 Jun 2020 02:39:46: 27000000 INFO @ Tue, 30 Jun 2020 02:39:49: 24000000 INFO @ Tue, 30 Jun 2020 02:39:50: 24000000 INFO @ Tue, 30 Jun 2020 02:39:54: 28000000 INFO @ Tue, 30 Jun 2020 02:39:56: 25000000 INFO @ Tue, 30 Jun 2020 02:39:57: 25000000 INFO @ Tue, 30 Jun 2020 02:40:02: 29000000 INFO @ Tue, 30 Jun 2020 02:40:04: 26000000 INFO @ Tue, 30 Jun 2020 02:40:05: 26000000 INFO @ Tue, 30 Jun 2020 02:40:11: 30000000 INFO @ Tue, 30 Jun 2020 02:40:12: 27000000 INFO @ Tue, 30 Jun 2020 02:40:13: 27000000 INFO @ Tue, 30 Jun 2020 02:40:19: 31000000 INFO @ Tue, 30 Jun 2020 02:40:20: 28000000 INFO @ Tue, 30 Jun 2020 02:40:21: 28000000 INFO @ Tue, 30 Jun 2020 02:40:27: 32000000 INFO @ Tue, 30 Jun 2020 02:40:28: 29000000 INFO @ Tue, 30 Jun 2020 02:40:29: 29000000 INFO @ Tue, 30 Jun 2020 02:40:35: 33000000 INFO @ Tue, 30 Jun 2020 02:40:37: 30000000 INFO @ Tue, 30 Jun 2020 02:40:37: 30000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:40:43: 34000000 INFO @ Tue, 30 Jun 2020 02:40:45: 31000000 INFO @ Tue, 30 Jun 2020 02:40:45: 31000000 INFO @ Tue, 30 Jun 2020 02:40:52: 35000000 INFO @ Tue, 30 Jun 2020 02:40:53: 32000000 INFO @ Tue, 30 Jun 2020 02:40:53: 32000000 INFO @ Tue, 30 Jun 2020 02:41:00: 36000000 INFO @ Tue, 30 Jun 2020 02:41:01: 33000000 INFO @ Tue, 30 Jun 2020 02:41:01: 33000000 INFO @ Tue, 30 Jun 2020 02:41:08: 37000000 INFO @ Tue, 30 Jun 2020 02:41:09: 34000000 INFO @ Tue, 30 Jun 2020 02:41:09: 34000000 INFO @ Tue, 30 Jun 2020 02:41:16: #1 tag size is determined as 100 bps INFO @ Tue, 30 Jun 2020 02:41:16: #1 tag size = 100 INFO @ Tue, 30 Jun 2020 02:41:16: #1 total tags in treatment: 37859749 INFO @ Tue, 30 Jun 2020 02:41:16: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:41:16: #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 02:41:17: #1 tags after filtering in treatment: 37859632 INFO @ Tue, 30 Jun 2020 02:41:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:41:17: #1 finished! INFO @ Tue, 30 Jun 2020 02:41:17: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:41:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:41:17: 35000000 INFO @ Tue, 30 Jun 2020 02:41:17: 35000000 INFO @ Tue, 30 Jun 2020 02:41:19: #2 number of paired peaks: 126 WARNING @ Tue, 30 Jun 2020 02:41:19: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Tue, 30 Jun 2020 02:41:19: start model_add_line... INFO @ Tue, 30 Jun 2020 02:41:19: start X-correlation... INFO @ Tue, 30 Jun 2020 02:41:19: end of X-cor INFO @ Tue, 30 Jun 2020 02:41:19: #2 finished! INFO @ Tue, 30 Jun 2020 02:41:19: #2 predicted fragment length is 73 bps INFO @ Tue, 30 Jun 2020 02:41:19: #2 alternative fragment length(s) may be 2,73 bps INFO @ Tue, 30 Jun 2020 02:41:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX201888/SRX201888.05_model.r WARNING @ Tue, 30 Jun 2020 02:41:19: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:41:19: #2 You may need to consider one of the other alternative d(s): 2,73 WARNING @ Tue, 30 Jun 2020 02:41:19: #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 02:41:19: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:41:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:41:25: 36000000 INFO @ Tue, 30 Jun 2020 02:41:26: 36000000 INFO @ Tue, 30 Jun 2020 02:41:34: 37000000 INFO @ Tue, 30 Jun 2020 02:41:34: 37000000 INFO @ Tue, 30 Jun 2020 02:41:41: #1 tag size is determined as 100 bps INFO @ Tue, 30 Jun 2020 02:41:41: #1 tag size = 100 INFO @ Tue, 30 Jun 2020 02:41:41: #1 total tags in treatment: 37859749 INFO @ Tue, 30 Jun 2020 02:41:41: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:41:41: #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 02:41:42: #1 tag size is determined as 100 bps INFO @ Tue, 30 Jun 2020 02:41:42: #1 tag size = 100 INFO @ Tue, 30 Jun 2020 02:41:42: #1 total tags in treatment: 37859749 INFO @ Tue, 30 Jun 2020 02:41:42: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:41:42: #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 02:41:42: #1 tags after filtering in treatment: 37859632 INFO @ Tue, 30 Jun 2020 02:41:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:41:42: #1 finished! INFO @ Tue, 30 Jun 2020 02:41:42: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:41:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:41:43: #1 tags after filtering in treatment: 37859632 INFO @ Tue, 30 Jun 2020 02:41:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:41:43: #1 finished! INFO @ Tue, 30 Jun 2020 02:41:43: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:41:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:41:45: #2 number of paired peaks: 126 WARNING @ Tue, 30 Jun 2020 02:41:45: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Tue, 30 Jun 2020 02:41:45: start model_add_line... INFO @ Tue, 30 Jun 2020 02:41:45: start X-correlation... INFO @ Tue, 30 Jun 2020 02:41:45: end of X-cor INFO @ Tue, 30 Jun 2020 02:41:45: #2 finished! INFO @ Tue, 30 Jun 2020 02:41:45: #2 predicted fragment length is 73 bps INFO @ Tue, 30 Jun 2020 02:41:45: #2 alternative fragment length(s) may be 2,73 bps INFO @ Tue, 30 Jun 2020 02:41:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX201888/SRX201888.10_model.r WARNING @ Tue, 30 Jun 2020 02:41:45: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:41:45: #2 You may need to consider one of the other alternative d(s): 2,73 WARNING @ Tue, 30 Jun 2020 02:41:45: #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 02:41:45: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:41:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:41:45: #2 number of paired peaks: 126 WARNING @ Tue, 30 Jun 2020 02:41:45: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Tue, 30 Jun 2020 02:41:45: start model_add_line... INFO @ Tue, 30 Jun 2020 02:41:45: start X-correlation... INFO @ Tue, 30 Jun 2020 02:41:45: end of X-cor INFO @ Tue, 30 Jun 2020 02:41:45: #2 finished! INFO @ Tue, 30 Jun 2020 02:41:45: #2 predicted fragment length is 73 bps INFO @ Tue, 30 Jun 2020 02:41:45: #2 alternative fragment length(s) may be 2,73 bps INFO @ Tue, 30 Jun 2020 02:41:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX201888/SRX201888.20_model.r WARNING @ Tue, 30 Jun 2020 02:41:45: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:41:45: #2 You may need to consider one of the other alternative d(s): 2,73 WARNING @ Tue, 30 Jun 2020 02:41:45: #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 02:41:45: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:41:45: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:42:21: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:42:46: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:42:47: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:42:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX201888/SRX201888.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:42:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX201888/SRX201888.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:42:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX201888/SRX201888.05_summits.bed INFO @ Tue, 30 Jun 2020 02:42:52: Done! pass1 - making usageList (753 chroms): 2 millis pass2 - checking and writing primary data (6175 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:43:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX201888/SRX201888.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:43:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX201888/SRX201888.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:43:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX201888/SRX201888.20_summits.bed INFO @ Tue, 30 Jun 2020 02:43:17: Done! INFO @ Tue, 30 Jun 2020 02:43:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX201888/SRX201888.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:43:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX201888/SRX201888.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:43:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX201888/SRX201888.10_summits.bed INFO @ Tue, 30 Jun 2020 02:43:17: Done! pass1 - making usageList (569 chroms): 2 millis pass2 - checking and writing primary data (1658 records, 4 fields): 17 millis pass1 - making usageList (681 chroms): 1 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (2716 records, 4 fields): 22 millis CompletedMACS2peakCalling