Job ID = 6529708 SRX = SRX3981720 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: 00:11:18 38799417 reads; of these: 38799417 (100.00%) were unpaired; of these: 1173985 (3.03%) aligned 0 times 27139917 (69.95%) aligned exactly 1 time 10485515 (27.02%) aligned >1 times 96.97% overall alignment rate Time searching: 00:11:18 Overall time: 00:11:18 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] 5277849 / 37625432 = 0.1403 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 03:41:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981720/SRX3981720.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981720/SRX3981720.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981720/SRX3981720.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981720/SRX3981720.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 03:41:47: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:41:47: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:41:53: 1000000 INFO @ Tue, 30 Jun 2020 03:41:59: 2000000 INFO @ Tue, 30 Jun 2020 03:42:05: 3000000 INFO @ Tue, 30 Jun 2020 03:42:11: 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 03:42:17: 5000000 INFO @ Tue, 30 Jun 2020 03:42:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981720/SRX3981720.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981720/SRX3981720.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981720/SRX3981720.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981720/SRX3981720.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 03:42:17: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:42:17: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:42:23: 6000000 INFO @ Tue, 30 Jun 2020 03:42:23: 1000000 INFO @ Tue, 30 Jun 2020 03:42:29: 7000000 INFO @ Tue, 30 Jun 2020 03:42:30: 2000000 INFO @ Tue, 30 Jun 2020 03:42:35: 8000000 INFO @ Tue, 30 Jun 2020 03:42:36: 3000000 INFO @ Tue, 30 Jun 2020 03:42:41: 9000000 INFO @ Tue, 30 Jun 2020 03:42:42: 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 @ Tue, 30 Jun 2020 03:42:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981720/SRX3981720.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981720/SRX3981720.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981720/SRX3981720.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981720/SRX3981720.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 03:42:47: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:42:47: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:42:47: 10000000 INFO @ Tue, 30 Jun 2020 03:42:49: 5000000 INFO @ Tue, 30 Jun 2020 03:42:54: 11000000 INFO @ Tue, 30 Jun 2020 03:42:54: 1000000 INFO @ Tue, 30 Jun 2020 03:42:55: 6000000 INFO @ Tue, 30 Jun 2020 03:43:01: 12000000 INFO @ Tue, 30 Jun 2020 03:43:01: 7000000 INFO @ Tue, 30 Jun 2020 03:43:01: 2000000 INFO @ Tue, 30 Jun 2020 03:43:07: 8000000 INFO @ Tue, 30 Jun 2020 03:43:08: 13000000 INFO @ Tue, 30 Jun 2020 03:43:08: 3000000 INFO @ Tue, 30 Jun 2020 03:43:14: 9000000 INFO @ Tue, 30 Jun 2020 03:43:14: 14000000 INFO @ Tue, 30 Jun 2020 03:43:15: 4000000 INFO @ Tue, 30 Jun 2020 03:43:20: 10000000 INFO @ Tue, 30 Jun 2020 03:43:21: 15000000 INFO @ Tue, 30 Jun 2020 03:43:22: 5000000 INFO @ Tue, 30 Jun 2020 03:43:26: 11000000 INFO @ Tue, 30 Jun 2020 03:43:28: 16000000 INFO @ Tue, 30 Jun 2020 03:43:28: 6000000 INFO @ Tue, 30 Jun 2020 03:43:32: 12000000 INFO @ Tue, 30 Jun 2020 03:43:35: 17000000 INFO @ Tue, 30 Jun 2020 03:43:35: 7000000 INFO @ Tue, 30 Jun 2020 03:43:39: 13000000 INFO @ Tue, 30 Jun 2020 03:43:42: 18000000 INFO @ Tue, 30 Jun 2020 03:43:42: 8000000 INFO @ Tue, 30 Jun 2020 03:43:45: 14000000 INFO @ Tue, 30 Jun 2020 03:43:49: 19000000 INFO @ Tue, 30 Jun 2020 03:43:49: 9000000 INFO @ Tue, 30 Jun 2020 03:43:53: 15000000 INFO @ Tue, 30 Jun 2020 03:43:56: 20000000 INFO @ Tue, 30 Jun 2020 03:43:56: 10000000 INFO @ Tue, 30 Jun 2020 03:43:59: 16000000 INFO @ Tue, 30 Jun 2020 03:44:02: 21000000 INFO @ Tue, 30 Jun 2020 03:44:03: 11000000 INFO @ Tue, 30 Jun 2020 03:44:06: 17000000 INFO @ Tue, 30 Jun 2020 03:44:09: 22000000 INFO @ Tue, 30 Jun 2020 03:44:10: 12000000 INFO @ Tue, 30 Jun 2020 03:44:12: 18000000 INFO @ Tue, 30 Jun 2020 03:44:15: 23000000 INFO @ Tue, 30 Jun 2020 03:44:16: 13000000 INFO @ Tue, 30 Jun 2020 03:44:19: 19000000 INFO @ Tue, 30 Jun 2020 03:44:22: 24000000 INFO @ Tue, 30 Jun 2020 03:44:23: 14000000 INFO @ Tue, 30 Jun 2020 03:44:26: 20000000 INFO @ Tue, 30 Jun 2020 03:44:29: 25000000 INFO @ Tue, 30 Jun 2020 03:44:30: 15000000 INFO @ Tue, 30 Jun 2020 03:44:33: 21000000 INFO @ Tue, 30 Jun 2020 03:44:35: 26000000 INFO @ Tue, 30 Jun 2020 03:44:37: 16000000 INFO @ Tue, 30 Jun 2020 03:44:40: 22000000 INFO @ Tue, 30 Jun 2020 03:44:42: 27000000 INFO @ Tue, 30 Jun 2020 03:44:44: 17000000 INFO @ Tue, 30 Jun 2020 03:44:47: 23000000 INFO @ Tue, 30 Jun 2020 03:44:50: 28000000 INFO @ Tue, 30 Jun 2020 03:44:50: 18000000 INFO @ Tue, 30 Jun 2020 03:44:54: 24000000 INFO @ Tue, 30 Jun 2020 03:44:57: 29000000 INFO @ Tue, 30 Jun 2020 03:44:57: 19000000 INFO @ Tue, 30 Jun 2020 03:45:01: 25000000 INFO @ Tue, 30 Jun 2020 03:45:04: 30000000 INFO @ Tue, 30 Jun 2020 03:45:05: 20000000 INFO @ Tue, 30 Jun 2020 03:45:08: 26000000 INFO @ Tue, 30 Jun 2020 03:45:11: 31000000 INFO @ Tue, 30 Jun 2020 03:45:12: 21000000 INFO @ Tue, 30 Jun 2020 03:45:15: 27000000 INFO @ Tue, 30 Jun 2020 03:45:19: 32000000 INFO @ Tue, 30 Jun 2020 03:45:19: 22000000 INFO @ Tue, 30 Jun 2020 03:45:22: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:45:22: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:45:22: #1 total tags in treatment: 32347583 INFO @ Tue, 30 Jun 2020 03:45:22: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:45:22: #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 03:45:23: #1 tags after filtering in treatment: 32347534 INFO @ Tue, 30 Jun 2020 03:45:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:45:23: #1 finished! INFO @ Tue, 30 Jun 2020 03:45:23: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:45:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:45:23: 28000000 INFO @ Tue, 30 Jun 2020 03:45:25: #2 number of paired peaks: 265 WARNING @ Tue, 30 Jun 2020 03:45:25: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Tue, 30 Jun 2020 03:45:25: start model_add_line... INFO @ Tue, 30 Jun 2020 03:45:25: start X-correlation... INFO @ Tue, 30 Jun 2020 03:45:25: end of X-cor INFO @ Tue, 30 Jun 2020 03:45:25: #2 finished! INFO @ Tue, 30 Jun 2020 03:45:25: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 03:45:25: #2 alternative fragment length(s) may be 1,50 bps INFO @ Tue, 30 Jun 2020 03:45:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981720/SRX3981720.05_model.r WARNING @ Tue, 30 Jun 2020 03:45:25: #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 03:45:25: #2 You may need to consider one of the other alternative d(s): 1,50 WARNING @ Tue, 30 Jun 2020 03:45:25: #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 03:45:25: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:45:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:45:27: 23000000 INFO @ Tue, 30 Jun 2020 03:45:30: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:45:34: 24000000 INFO @ Tue, 30 Jun 2020 03:45:37: 30000000 INFO @ Tue, 30 Jun 2020 03:45:42: 25000000 INFO @ Tue, 30 Jun 2020 03:45:45: 31000000 INFO @ Tue, 30 Jun 2020 03:45:49: 26000000 INFO @ Tue, 30 Jun 2020 03:45:52: 32000000 INFO @ Tue, 30 Jun 2020 03:45:55: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:45:55: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:45:55: #1 total tags in treatment: 32347583 INFO @ Tue, 30 Jun 2020 03:45:55: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:45:55: #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 03:45:56: #1 tags after filtering in treatment: 32347534 INFO @ Tue, 30 Jun 2020 03:45:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:45:56: #1 finished! INFO @ Tue, 30 Jun 2020 03:45:56: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:45:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:45:57: 27000000 INFO @ Tue, 30 Jun 2020 03:45:58: #2 number of paired peaks: 265 WARNING @ Tue, 30 Jun 2020 03:45:58: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Tue, 30 Jun 2020 03:45:58: start model_add_line... INFO @ Tue, 30 Jun 2020 03:45:59: start X-correlation... INFO @ Tue, 30 Jun 2020 03:45:59: end of X-cor INFO @ Tue, 30 Jun 2020 03:45:59: #2 finished! INFO @ Tue, 30 Jun 2020 03:45:59: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 03:45:59: #2 alternative fragment length(s) may be 1,50 bps INFO @ Tue, 30 Jun 2020 03:45:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981720/SRX3981720.10_model.r WARNING @ Tue, 30 Jun 2020 03:45:59: #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 03:45:59: #2 You may need to consider one of the other alternative d(s): 1,50 WARNING @ Tue, 30 Jun 2020 03:45:59: #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 03:45:59: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:45:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:46:06: 28000000 INFO @ Tue, 30 Jun 2020 03:46:13: 29000000 INFO @ Tue, 30 Jun 2020 03:46:17: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:46:21: 30000000 INFO @ Tue, 30 Jun 2020 03:46:29: 31000000 INFO @ Tue, 30 Jun 2020 03:46:37: 32000000 INFO @ Tue, 30 Jun 2020 03:46:39: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:46:39: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:46:39: #1 total tags in treatment: 32347583 INFO @ Tue, 30 Jun 2020 03:46:39: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:46:39: #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 03:46:41: #1 tags after filtering in treatment: 32347534 INFO @ Tue, 30 Jun 2020 03:46:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:46:41: #1 finished! INFO @ Tue, 30 Jun 2020 03:46:41: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:46:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:46:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981720/SRX3981720.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:46:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981720/SRX3981720.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:46:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981720/SRX3981720.05_summits.bed INFO @ Tue, 30 Jun 2020 03:46:42: Done! INFO @ Tue, 30 Jun 2020 03:46:43: #2 number of paired peaks: 265 WARNING @ Tue, 30 Jun 2020 03:46:43: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Tue, 30 Jun 2020 03:46:43: start model_add_line... pass1 - making usageList (660 chroms): 2 millis pass2 - checking and writing primary data (3067 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:46:43: start X-correlation... INFO @ Tue, 30 Jun 2020 03:46:43: end of X-cor INFO @ Tue, 30 Jun 2020 03:46:43: #2 finished! INFO @ Tue, 30 Jun 2020 03:46:43: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 03:46:43: #2 alternative fragment length(s) may be 1,50 bps INFO @ Tue, 30 Jun 2020 03:46:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981720/SRX3981720.20_model.r WARNING @ Tue, 30 Jun 2020 03:46:43: #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 03:46:43: #2 You may need to consider one of the other alternative d(s): 1,50 WARNING @ Tue, 30 Jun 2020 03:46:43: #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 03:46:43: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:46:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:46:50: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:47:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981720/SRX3981720.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:47:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981720/SRX3981720.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:47:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981720/SRX3981720.10_summits.bed INFO @ Tue, 30 Jun 2020 03:47:15: Done! pass1 - making usageList (543 chroms): 2 millis pass2 - checking and writing primary data (2224 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:47:34: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:47:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981720/SRX3981720.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:47:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981720/SRX3981720.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:47:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981720/SRX3981720.20_summits.bed INFO @ Tue, 30 Jun 2020 03:47:59: Done! pass1 - making usageList (360 chroms): 2 millis pass2 - checking and writing primary data (935 records, 4 fields): 21 millis CompletedMACS2peakCalling