Job ID = 6529699 SRX = SRX3981695 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: 00:09:47 38376445 reads; of these: 38376445 (100.00%) were unpaired; of these: 1079554 (2.81%) aligned 0 times 28296898 (73.74%) aligned exactly 1 time 8999993 (23.45%) aligned >1 times 97.19% overall alignment rate Time searching: 00:09:47 Overall time: 00:09:47 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] 5278792 / 37296891 = 0.1415 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 03:14:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981695/SRX3981695.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981695/SRX3981695.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981695/SRX3981695.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981695/SRX3981695.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 03:14:54: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:14:54: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:15:02: 1000000 INFO @ Tue, 30 Jun 2020 03:15:09: 2000000 INFO @ Tue, 30 Jun 2020 03:15:16: 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 03:15:23: 4000000 INFO @ Tue, 30 Jun 2020 03:15:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981695/SRX3981695.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981695/SRX3981695.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981695/SRX3981695.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981695/SRX3981695.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 03:15:24: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:15:24: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:15:31: 5000000 INFO @ Tue, 30 Jun 2020 03:15:32: 1000000 INFO @ Tue, 30 Jun 2020 03:15:39: 6000000 INFO @ Tue, 30 Jun 2020 03:15:40: 2000000 INFO @ Tue, 30 Jun 2020 03:15:47: 7000000 INFO @ Tue, 30 Jun 2020 03:15:48: 3000000 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 03:15:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981695/SRX3981695.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981695/SRX3981695.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981695/SRX3981695.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981695/SRX3981695.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 03:15:54: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:15:54: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:15:55: 8000000 INFO @ Tue, 30 Jun 2020 03:15:56: 4000000 INFO @ Tue, 30 Jun 2020 03:16:02: 1000000 INFO @ Tue, 30 Jun 2020 03:16:03: 9000000 INFO @ Tue, 30 Jun 2020 03:16:04: 5000000 INFO @ Tue, 30 Jun 2020 03:16:11: 2000000 INFO @ Tue, 30 Jun 2020 03:16:11: 10000000 INFO @ Tue, 30 Jun 2020 03:16:13: 6000000 INFO @ Tue, 30 Jun 2020 03:16:19: 3000000 INFO @ Tue, 30 Jun 2020 03:16:19: 11000000 INFO @ Tue, 30 Jun 2020 03:16:21: 7000000 INFO @ Tue, 30 Jun 2020 03:16:27: 4000000 INFO @ Tue, 30 Jun 2020 03:16:28: 12000000 INFO @ Tue, 30 Jun 2020 03:16:29: 8000000 INFO @ Tue, 30 Jun 2020 03:16:35: 5000000 INFO @ Tue, 30 Jun 2020 03:16:36: 13000000 INFO @ Tue, 30 Jun 2020 03:16:37: 9000000 INFO @ Tue, 30 Jun 2020 03:16:43: 6000000 INFO @ Tue, 30 Jun 2020 03:16:43: 14000000 INFO @ Tue, 30 Jun 2020 03:16:45: 10000000 INFO @ Tue, 30 Jun 2020 03:16:51: 7000000 INFO @ Tue, 30 Jun 2020 03:16:52: 15000000 INFO @ Tue, 30 Jun 2020 03:16:53: 11000000 INFO @ Tue, 30 Jun 2020 03:16:59: 8000000 INFO @ Tue, 30 Jun 2020 03:17:00: 16000000 INFO @ Tue, 30 Jun 2020 03:17:01: 12000000 INFO @ Tue, 30 Jun 2020 03:17:07: 9000000 INFO @ Tue, 30 Jun 2020 03:17:08: 17000000 INFO @ Tue, 30 Jun 2020 03:17:09: 13000000 INFO @ Tue, 30 Jun 2020 03:17:16: 10000000 INFO @ Tue, 30 Jun 2020 03:17:17: 18000000 INFO @ Tue, 30 Jun 2020 03:17:17: 14000000 INFO @ Tue, 30 Jun 2020 03:17:24: 11000000 INFO @ Tue, 30 Jun 2020 03:17:25: 15000000 INFO @ Tue, 30 Jun 2020 03:17:25: 19000000 INFO @ Tue, 30 Jun 2020 03:17:32: 12000000 INFO @ Tue, 30 Jun 2020 03:17:33: 16000000 INFO @ Tue, 30 Jun 2020 03:17:33: 20000000 INFO @ Tue, 30 Jun 2020 03:17:40: 13000000 INFO @ Tue, 30 Jun 2020 03:17:41: 17000000 INFO @ Tue, 30 Jun 2020 03:17:41: 21000000 INFO @ Tue, 30 Jun 2020 03:17:48: 14000000 INFO @ Tue, 30 Jun 2020 03:17:49: 18000000 INFO @ Tue, 30 Jun 2020 03:17:49: 22000000 INFO @ Tue, 30 Jun 2020 03:17:56: 15000000 INFO @ Tue, 30 Jun 2020 03:17:57: 19000000 INFO @ Tue, 30 Jun 2020 03:17:58: 23000000 INFO @ Tue, 30 Jun 2020 03:18:05: 16000000 INFO @ Tue, 30 Jun 2020 03:18:05: 20000000 INFO @ Tue, 30 Jun 2020 03:18:06: 24000000 INFO @ Tue, 30 Jun 2020 03:18:13: 17000000 INFO @ Tue, 30 Jun 2020 03:18:13: 21000000 INFO @ Tue, 30 Jun 2020 03:18:14: 25000000 INFO @ Tue, 30 Jun 2020 03:18:21: 22000000 INFO @ Tue, 30 Jun 2020 03:18:21: 18000000 INFO @ Tue, 30 Jun 2020 03:18:22: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:18:29: 23000000 INFO @ Tue, 30 Jun 2020 03:18:29: 19000000 INFO @ Tue, 30 Jun 2020 03:18:30: 27000000 INFO @ Tue, 30 Jun 2020 03:18:37: 24000000 INFO @ Tue, 30 Jun 2020 03:18:37: 20000000 INFO @ Tue, 30 Jun 2020 03:18:38: 28000000 INFO @ Tue, 30 Jun 2020 03:18:45: 25000000 INFO @ Tue, 30 Jun 2020 03:18:45: 21000000 INFO @ Tue, 30 Jun 2020 03:18:46: 29000000 INFO @ Tue, 30 Jun 2020 03:18:53: 26000000 INFO @ Tue, 30 Jun 2020 03:18:54: 22000000 INFO @ Tue, 30 Jun 2020 03:18:54: 30000000 INFO @ Tue, 30 Jun 2020 03:19:01: 27000000 INFO @ Tue, 30 Jun 2020 03:19:02: 23000000 INFO @ Tue, 30 Jun 2020 03:19:02: 31000000 INFO @ Tue, 30 Jun 2020 03:19:09: 28000000 INFO @ Tue, 30 Jun 2020 03:19:10: 24000000 INFO @ Tue, 30 Jun 2020 03:19:10: 32000000 INFO @ Tue, 30 Jun 2020 03:19:11: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:19:11: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:19:11: #1 total tags in treatment: 32018099 INFO @ Tue, 30 Jun 2020 03:19:11: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:19:11: #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 03:19:11: #1 tags after filtering in treatment: 32018049 INFO @ Tue, 30 Jun 2020 03:19:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:19:11: #1 finished! INFO @ Tue, 30 Jun 2020 03:19:11: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:19:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:19:13: #2 number of paired peaks: 154 WARNING @ Tue, 30 Jun 2020 03:19:13: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Tue, 30 Jun 2020 03:19:13: start model_add_line... INFO @ Tue, 30 Jun 2020 03:19:13: start X-correlation... INFO @ Tue, 30 Jun 2020 03:19:13: end of X-cor INFO @ Tue, 30 Jun 2020 03:19:13: #2 finished! INFO @ Tue, 30 Jun 2020 03:19:13: #2 predicted fragment length is 52 bps INFO @ Tue, 30 Jun 2020 03:19:13: #2 alternative fragment length(s) may be 1,52,545,552 bps INFO @ Tue, 30 Jun 2020 03:19:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981695/SRX3981695.05_model.r WARNING @ Tue, 30 Jun 2020 03:19:13: #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 03:19:13: #2 You may need to consider one of the other alternative d(s): 1,52,545,552 WARNING @ Tue, 30 Jun 2020 03:19:13: #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 03:19:13: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:19:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:19:16: 29000000 INFO @ Tue, 30 Jun 2020 03:19:18: 25000000 INFO @ Tue, 30 Jun 2020 03:19:24: 30000000 INFO @ Tue, 30 Jun 2020 03:19:25: 26000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:19:32: 31000000 INFO @ Tue, 30 Jun 2020 03:19:33: 27000000 INFO @ Tue, 30 Jun 2020 03:19:40: 32000000 INFO @ Tue, 30 Jun 2020 03:19:40: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:19:40: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:19:40: #1 total tags in treatment: 32018099 INFO @ Tue, 30 Jun 2020 03:19:40: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:19:40: #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 03:19:41: #1 tags after filtering in treatment: 32018049 INFO @ Tue, 30 Jun 2020 03:19:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:19:41: #1 finished! INFO @ Tue, 30 Jun 2020 03:19:41: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:19:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:19:41: 28000000 INFO @ Tue, 30 Jun 2020 03:19:43: #2 number of paired peaks: 154 WARNING @ Tue, 30 Jun 2020 03:19:43: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Tue, 30 Jun 2020 03:19:43: start model_add_line... INFO @ Tue, 30 Jun 2020 03:19:43: start X-correlation... INFO @ Tue, 30 Jun 2020 03:19:43: end of X-cor INFO @ Tue, 30 Jun 2020 03:19:43: #2 finished! INFO @ Tue, 30 Jun 2020 03:19:43: #2 predicted fragment length is 52 bps INFO @ Tue, 30 Jun 2020 03:19:43: #2 alternative fragment length(s) may be 1,52,545,552 bps INFO @ Tue, 30 Jun 2020 03:19:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981695/SRX3981695.10_model.r WARNING @ Tue, 30 Jun 2020 03:19:43: #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 03:19:43: #2 You may need to consider one of the other alternative d(s): 1,52,545,552 WARNING @ Tue, 30 Jun 2020 03:19:43: #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 03:19:43: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:19:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:19:49: 29000000 INFO @ Tue, 30 Jun 2020 03:19:56: 30000000 INFO @ Tue, 30 Jun 2020 03:20:03: 31000000 INFO @ Tue, 30 Jun 2020 03:20:06: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:20:10: 32000000 INFO @ Tue, 30 Jun 2020 03:20:11: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:20:11: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:20:11: #1 total tags in treatment: 32018099 INFO @ Tue, 30 Jun 2020 03:20:11: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:20:11: #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 03:20:11: #1 tags after filtering in treatment: 32018049 INFO @ Tue, 30 Jun 2020 03:20:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:20:11: #1 finished! INFO @ Tue, 30 Jun 2020 03:20:11: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:20:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:20:13: #2 number of paired peaks: 154 WARNING @ Tue, 30 Jun 2020 03:20:13: Fewer paired peaks (154) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 154 pairs to build model! INFO @ Tue, 30 Jun 2020 03:20:13: start model_add_line... INFO @ Tue, 30 Jun 2020 03:20:14: start X-correlation... INFO @ Tue, 30 Jun 2020 03:20:14: end of X-cor INFO @ Tue, 30 Jun 2020 03:20:14: #2 finished! INFO @ Tue, 30 Jun 2020 03:20:14: #2 predicted fragment length is 52 bps INFO @ Tue, 30 Jun 2020 03:20:14: #2 alternative fragment length(s) may be 1,52,545,552 bps INFO @ Tue, 30 Jun 2020 03:20:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981695/SRX3981695.20_model.r WARNING @ Tue, 30 Jun 2020 03:20:14: #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 03:20:14: #2 You may need to consider one of the other alternative d(s): 1,52,545,552 WARNING @ Tue, 30 Jun 2020 03:20:14: #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 03:20:14: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:20:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:20:33: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:20:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981695/SRX3981695.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:20:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981695/SRX3981695.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:20:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981695/SRX3981695.05_summits.bed INFO @ Tue, 30 Jun 2020 03:20:34: Done! pass1 - making usageList (676 chroms): 1 millis pass2 - checking and writing primary data (3559 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:20:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981695/SRX3981695.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:20:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981695/SRX3981695.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:20:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981695/SRX3981695.10_summits.bed INFO @ Tue, 30 Jun 2020 03:20:58: Done! pass1 - making usageList (475 chroms): 2 millis pass2 - checking and writing primary data (1699 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:21:06: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:21:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981695/SRX3981695.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:21:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981695/SRX3981695.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:21:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981695/SRX3981695.20_summits.bed INFO @ Tue, 30 Jun 2020 03:21:33: Done! pass1 - making usageList (229 chroms): 1 millis pass2 - checking and writing primary data (536 records, 4 fields): 7 millis CompletedMACS2peakCalling