Job ID = 6529670 SRX = SRX3981633 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: 00:10:07 39670626 reads; of these: 39670626 (100.00%) were unpaired; of these: 1031336 (2.60%) aligned 0 times 30187312 (76.09%) aligned exactly 1 time 8451978 (21.31%) aligned >1 times 97.40% overall alignment rate Time searching: 00:10:07 Overall time: 00:10:07 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] 5246002 / 38639290 = 0.1358 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 02:46:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981633/SRX3981633.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981633/SRX3981633.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981633/SRX3981633.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981633/SRX3981633.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 02:46:01: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:46:01: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:46:08: 1000000 INFO @ Tue, 30 Jun 2020 02:46:15: 2000000 INFO @ Tue, 30 Jun 2020 02:46:22: 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 02:46:29: 4000000 INFO @ Tue, 30 Jun 2020 02:46:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981633/SRX3981633.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981633/SRX3981633.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981633/SRX3981633.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981633/SRX3981633.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 02:46:31: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:46:31: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:46:37: 5000000 INFO @ Tue, 30 Jun 2020 02:46:38: 1000000 INFO @ Tue, 30 Jun 2020 02:46:45: 2000000 INFO @ Tue, 30 Jun 2020 02:46:45: 6000000 INFO @ Tue, 30 Jun 2020 02:46:51: 3000000 INFO @ Tue, 30 Jun 2020 02:46:53: 7000000 INFO @ Tue, 30 Jun 2020 02:46:58: 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 02:47:01: 8000000 INFO @ Tue, 30 Jun 2020 02:47:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981633/SRX3981633.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981633/SRX3981633.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981633/SRX3981633.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981633/SRX3981633.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 02:47:01: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:47:01: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:47:05: 5000000 INFO @ Tue, 30 Jun 2020 02:47:08: 1000000 INFO @ Tue, 30 Jun 2020 02:47:09: 9000000 INFO @ Tue, 30 Jun 2020 02:47:13: 6000000 INFO @ Tue, 30 Jun 2020 02:47:15: 2000000 INFO @ Tue, 30 Jun 2020 02:47:16: 10000000 INFO @ Tue, 30 Jun 2020 02:47:20: 7000000 INFO @ Tue, 30 Jun 2020 02:47:22: 3000000 INFO @ Tue, 30 Jun 2020 02:47:24: 11000000 INFO @ Tue, 30 Jun 2020 02:47:27: 8000000 INFO @ Tue, 30 Jun 2020 02:47:30: 4000000 INFO @ Tue, 30 Jun 2020 02:47:32: 12000000 INFO @ Tue, 30 Jun 2020 02:47:34: 9000000 INFO @ Tue, 30 Jun 2020 02:47:37: 5000000 INFO @ Tue, 30 Jun 2020 02:47:40: 13000000 INFO @ Tue, 30 Jun 2020 02:47:42: 10000000 INFO @ Tue, 30 Jun 2020 02:47:44: 6000000 INFO @ Tue, 30 Jun 2020 02:47:48: 14000000 INFO @ Tue, 30 Jun 2020 02:47:49: 11000000 INFO @ Tue, 30 Jun 2020 02:47:52: 7000000 INFO @ Tue, 30 Jun 2020 02:47:56: 15000000 INFO @ Tue, 30 Jun 2020 02:47:56: 12000000 INFO @ Tue, 30 Jun 2020 02:47:59: 8000000 INFO @ Tue, 30 Jun 2020 02:48:04: 13000000 INFO @ Tue, 30 Jun 2020 02:48:04: 16000000 INFO @ Tue, 30 Jun 2020 02:48:06: 9000000 INFO @ Tue, 30 Jun 2020 02:48:11: 14000000 INFO @ Tue, 30 Jun 2020 02:48:12: 17000000 INFO @ Tue, 30 Jun 2020 02:48:14: 10000000 INFO @ Tue, 30 Jun 2020 02:48:18: 15000000 INFO @ Tue, 30 Jun 2020 02:48:20: 18000000 INFO @ Tue, 30 Jun 2020 02:48:21: 11000000 INFO @ Tue, 30 Jun 2020 02:48:26: 16000000 INFO @ Tue, 30 Jun 2020 02:48:28: 19000000 INFO @ Tue, 30 Jun 2020 02:48:28: 12000000 INFO @ Tue, 30 Jun 2020 02:48:33: 17000000 INFO @ Tue, 30 Jun 2020 02:48:36: 13000000 INFO @ Tue, 30 Jun 2020 02:48:36: 20000000 INFO @ Tue, 30 Jun 2020 02:48:41: 18000000 INFO @ Tue, 30 Jun 2020 02:48:43: 14000000 INFO @ Tue, 30 Jun 2020 02:48:44: 21000000 INFO @ Tue, 30 Jun 2020 02:48:48: 19000000 INFO @ Tue, 30 Jun 2020 02:48:50: 15000000 INFO @ Tue, 30 Jun 2020 02:48:52: 22000000 INFO @ Tue, 30 Jun 2020 02:48:56: 20000000 INFO @ Tue, 30 Jun 2020 02:48:58: 16000000 INFO @ Tue, 30 Jun 2020 02:49:01: 23000000 INFO @ Tue, 30 Jun 2020 02:49:03: 21000000 INFO @ Tue, 30 Jun 2020 02:49:05: 17000000 INFO @ Tue, 30 Jun 2020 02:49:09: 24000000 INFO @ Tue, 30 Jun 2020 02:49:11: 22000000 INFO @ Tue, 30 Jun 2020 02:49:13: 18000000 INFO @ Tue, 30 Jun 2020 02:49:17: 25000000 INFO @ Tue, 30 Jun 2020 02:49:19: 23000000 INFO @ Tue, 30 Jun 2020 02:49:20: 19000000 INFO @ Tue, 30 Jun 2020 02:49:25: 26000000 INFO @ Tue, 30 Jun 2020 02:49:26: 24000000 INFO @ Tue, 30 Jun 2020 02:49:28: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:49:33: 27000000 INFO @ Tue, 30 Jun 2020 02:49:34: 25000000 INFO @ Tue, 30 Jun 2020 02:49:36: 21000000 INFO @ Tue, 30 Jun 2020 02:49:41: 28000000 INFO @ Tue, 30 Jun 2020 02:49:41: 26000000 INFO @ Tue, 30 Jun 2020 02:49:43: 22000000 INFO @ Tue, 30 Jun 2020 02:49:49: 27000000 INFO @ Tue, 30 Jun 2020 02:49:50: 29000000 INFO @ Tue, 30 Jun 2020 02:49:51: 23000000 INFO @ Tue, 30 Jun 2020 02:49:57: 28000000 INFO @ Tue, 30 Jun 2020 02:49:58: 30000000 INFO @ Tue, 30 Jun 2020 02:49:58: 24000000 INFO @ Tue, 30 Jun 2020 02:50:05: 29000000 INFO @ Tue, 30 Jun 2020 02:50:06: 25000000 INFO @ Tue, 30 Jun 2020 02:50:06: 31000000 INFO @ Tue, 30 Jun 2020 02:50:12: 30000000 INFO @ Tue, 30 Jun 2020 02:50:13: 26000000 INFO @ Tue, 30 Jun 2020 02:50:14: 32000000 INFO @ Tue, 30 Jun 2020 02:50:20: 31000000 INFO @ Tue, 30 Jun 2020 02:50:20: 27000000 INFO @ Tue, 30 Jun 2020 02:50:23: 33000000 INFO @ Tue, 30 Jun 2020 02:50:26: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:50:26: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:50:26: #1 total tags in treatment: 33393288 INFO @ Tue, 30 Jun 2020 02:50:26: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:50:26: #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 02:50:27: #1 tags after filtering in treatment: 33393249 INFO @ Tue, 30 Jun 2020 02:50:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:50:27: #1 finished! INFO @ Tue, 30 Jun 2020 02:50:27: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:50:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:50:27: 32000000 INFO @ Tue, 30 Jun 2020 02:50:28: 28000000 INFO @ Tue, 30 Jun 2020 02:50:29: #2 number of paired peaks: 155 WARNING @ Tue, 30 Jun 2020 02:50:29: Fewer paired peaks (155) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 155 pairs to build model! INFO @ Tue, 30 Jun 2020 02:50:29: start model_add_line... INFO @ Tue, 30 Jun 2020 02:50:29: start X-correlation... INFO @ Tue, 30 Jun 2020 02:50:29: end of X-cor INFO @ Tue, 30 Jun 2020 02:50:29: #2 finished! INFO @ Tue, 30 Jun 2020 02:50:29: #2 predicted fragment length is 53 bps INFO @ Tue, 30 Jun 2020 02:50:29: #2 alternative fragment length(s) may be 1,53,109,541,560,567 bps INFO @ Tue, 30 Jun 2020 02:50:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981633/SRX3981633.05_model.r WARNING @ Tue, 30 Jun 2020 02:50:29: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:50:29: #2 You may need to consider one of the other alternative d(s): 1,53,109,541,560,567 WARNING @ Tue, 30 Jun 2020 02:50:29: #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 02:50:29: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:50:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:50:34: 33000000 INFO @ Tue, 30 Jun 2020 02:50:35: 29000000 INFO @ Tue, 30 Jun 2020 02:50:37: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:50:37: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:50:37: #1 total tags in treatment: 33393288 INFO @ Tue, 30 Jun 2020 02:50:37: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:50:37: #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 02:50:38: #1 tags after filtering in treatment: 33393249 INFO @ Tue, 30 Jun 2020 02:50:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:50:38: #1 finished! INFO @ Tue, 30 Jun 2020 02:50:38: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:50:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:50:41: #2 number of paired peaks: 155 WARNING @ Tue, 30 Jun 2020 02:50:41: Fewer paired peaks (155) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 155 pairs to build model! INFO @ Tue, 30 Jun 2020 02:50:41: start model_add_line... INFO @ Tue, 30 Jun 2020 02:50:41: start X-correlation... INFO @ Tue, 30 Jun 2020 02:50:41: end of X-cor INFO @ Tue, 30 Jun 2020 02:50:41: #2 finished! INFO @ Tue, 30 Jun 2020 02:50:41: #2 predicted fragment length is 53 bps INFO @ Tue, 30 Jun 2020 02:50:41: #2 alternative fragment length(s) may be 1,53,109,541,560,567 bps INFO @ Tue, 30 Jun 2020 02:50:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981633/SRX3981633.10_model.r WARNING @ Tue, 30 Jun 2020 02:50:41: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:50:41: #2 You may need to consider one of the other alternative d(s): 1,53,109,541,560,567 WARNING @ Tue, 30 Jun 2020 02:50:41: #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 02:50:41: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:50:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:50:42: 30000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:50:48: 31000000 INFO @ Tue, 30 Jun 2020 02:50:54: 32000000 INFO @ Tue, 30 Jun 2020 02:51:00: 33000000 INFO @ Tue, 30 Jun 2020 02:51:03: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:51:03: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:51:03: #1 total tags in treatment: 33393288 INFO @ Tue, 30 Jun 2020 02:51:03: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:51:03: #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 02:51:04: #1 tags after filtering in treatment: 33393249 INFO @ Tue, 30 Jun 2020 02:51:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:51:04: #1 finished! INFO @ Tue, 30 Jun 2020 02:51:04: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:51:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:51:06: #2 number of paired peaks: 155 WARNING @ Tue, 30 Jun 2020 02:51:06: Fewer paired peaks (155) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 155 pairs to build model! INFO @ Tue, 30 Jun 2020 02:51:06: start model_add_line... INFO @ Tue, 30 Jun 2020 02:51:07: start X-correlation... INFO @ Tue, 30 Jun 2020 02:51:07: end of X-cor INFO @ Tue, 30 Jun 2020 02:51:07: #2 finished! INFO @ Tue, 30 Jun 2020 02:51:07: #2 predicted fragment length is 53 bps INFO @ Tue, 30 Jun 2020 02:51:07: #2 alternative fragment length(s) may be 1,53,109,541,560,567 bps INFO @ Tue, 30 Jun 2020 02:51:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981633/SRX3981633.20_model.r WARNING @ Tue, 30 Jun 2020 02:51:07: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:51:07: #2 You may need to consider one of the other alternative d(s): 1,53,109,541,560,567 WARNING @ Tue, 30 Jun 2020 02:51:07: #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 02:51:07: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:51:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:51:29: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:51:43: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:52:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981633/SRX3981633.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:52:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981633/SRX3981633.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:52:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981633/SRX3981633.05_summits.bed INFO @ Tue, 30 Jun 2020 02:52:01: Done! pass1 - making usageList (633 chroms): 1 millis pass2 - checking and writing primary data (3851 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:52:08: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:52:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981633/SRX3981633.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:52:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981633/SRX3981633.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:52:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981633/SRX3981633.10_summits.bed INFO @ Tue, 30 Jun 2020 02:52:13: Done! pass1 - making usageList (366 chroms): 1 millis pass2 - checking and writing primary data (1532 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:52:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981633/SRX3981633.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:52:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981633/SRX3981633.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:52:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981633/SRX3981633.20_summits.bed INFO @ Tue, 30 Jun 2020 02:52:39: Done! pass1 - making usageList (144 chroms): 1 millis pass2 - checking and writing primary data (415 records, 4 fields): 7 millis CompletedMACS2peakCalling