Job ID = 6529790 SRX = SRX4828020 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: 00:10:59 40815124 reads; of these: 40815124 (100.00%) were unpaired; of these: 1641968 (4.02%) aligned 0 times 31410943 (76.96%) aligned exactly 1 time 7762213 (19.02%) aligned >1 times 95.98% overall alignment rate Time searching: 00:10:59 Overall time: 00:10:59 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] 8348150 / 39173156 = 0.2131 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 02:52:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4828020/SRX4828020.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4828020/SRX4828020.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4828020/SRX4828020.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4828020/SRX4828020.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 02:52:07: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:52:07: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:52:12: 1000000 INFO @ Tue, 30 Jun 2020 02:52:18: 2000000 INFO @ Tue, 30 Jun 2020 02:52:23: 3000000 INFO @ Tue, 30 Jun 2020 02:52:29: 4000000 INFO @ Tue, 30 Jun 2020 02:52:34: 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 02:52:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4828020/SRX4828020.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4828020/SRX4828020.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4828020/SRX4828020.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4828020/SRX4828020.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 02:52:36: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:52:36: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:52:40: 6000000 INFO @ Tue, 30 Jun 2020 02:52:43: 1000000 INFO @ Tue, 30 Jun 2020 02:52:46: 7000000 INFO @ Tue, 30 Jun 2020 02:52:49: 2000000 INFO @ Tue, 30 Jun 2020 02:52:52: 8000000 INFO @ Tue, 30 Jun 2020 02:52:55: 3000000 INFO @ Tue, 30 Jun 2020 02:52:58: 9000000 INFO @ Tue, 30 Jun 2020 02:53:00: 4000000 INFO @ Tue, 30 Jun 2020 02:53:04: 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 02:53:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4828020/SRX4828020.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4828020/SRX4828020.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4828020/SRX4828020.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4828020/SRX4828020.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 02:53:06: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:53:06: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:53:06: 5000000 INFO @ Tue, 30 Jun 2020 02:53:10: 11000000 INFO @ Tue, 30 Jun 2020 02:53:12: 6000000 INFO @ Tue, 30 Jun 2020 02:53:13: 1000000 INFO @ Tue, 30 Jun 2020 02:53:15: 12000000 INFO @ Tue, 30 Jun 2020 02:53:18: 7000000 INFO @ Tue, 30 Jun 2020 02:53:19: 2000000 INFO @ Tue, 30 Jun 2020 02:53:21: 13000000 INFO @ Tue, 30 Jun 2020 02:53:24: 8000000 INFO @ Tue, 30 Jun 2020 02:53:24: 3000000 INFO @ Tue, 30 Jun 2020 02:53:27: 14000000 INFO @ Tue, 30 Jun 2020 02:53:30: 9000000 INFO @ Tue, 30 Jun 2020 02:53:30: 4000000 INFO @ Tue, 30 Jun 2020 02:53:33: 15000000 INFO @ Tue, 30 Jun 2020 02:53:36: 10000000 INFO @ Tue, 30 Jun 2020 02:53:36: 5000000 INFO @ Tue, 30 Jun 2020 02:53:39: 16000000 INFO @ Tue, 30 Jun 2020 02:53:42: 11000000 INFO @ Tue, 30 Jun 2020 02:53:42: 6000000 INFO @ Tue, 30 Jun 2020 02:53:45: 17000000 INFO @ Tue, 30 Jun 2020 02:53:48: 12000000 INFO @ Tue, 30 Jun 2020 02:53:48: 7000000 INFO @ Tue, 30 Jun 2020 02:53:51: 18000000 INFO @ Tue, 30 Jun 2020 02:53:54: 13000000 INFO @ Tue, 30 Jun 2020 02:53:54: 8000000 INFO @ Tue, 30 Jun 2020 02:53:57: 19000000 INFO @ Tue, 30 Jun 2020 02:54:00: 9000000 INFO @ Tue, 30 Jun 2020 02:54:00: 14000000 INFO @ Tue, 30 Jun 2020 02:54:03: 20000000 INFO @ Tue, 30 Jun 2020 02:54:06: 10000000 INFO @ Tue, 30 Jun 2020 02:54:06: 15000000 INFO @ Tue, 30 Jun 2020 02:54:10: 21000000 INFO @ Tue, 30 Jun 2020 02:54:12: 11000000 INFO @ Tue, 30 Jun 2020 02:54:12: 16000000 INFO @ Tue, 30 Jun 2020 02:54:16: 22000000 INFO @ Tue, 30 Jun 2020 02:54:19: 12000000 INFO @ Tue, 30 Jun 2020 02:54:19: 17000000 INFO @ Tue, 30 Jun 2020 02:54:23: 23000000 INFO @ Tue, 30 Jun 2020 02:54:25: 13000000 INFO @ Tue, 30 Jun 2020 02:54:25: 18000000 INFO @ Tue, 30 Jun 2020 02:54:29: 24000000 INFO @ Tue, 30 Jun 2020 02:54:31: 14000000 INFO @ Tue, 30 Jun 2020 02:54:31: 19000000 INFO @ Tue, 30 Jun 2020 02:54:36: 25000000 INFO @ Tue, 30 Jun 2020 02:54:37: 15000000 INFO @ Tue, 30 Jun 2020 02:54:38: 20000000 INFO @ Tue, 30 Jun 2020 02:54:42: 26000000 INFO @ Tue, 30 Jun 2020 02:54:43: 16000000 INFO @ Tue, 30 Jun 2020 02:54:44: 21000000 INFO @ Tue, 30 Jun 2020 02:54:48: 27000000 INFO @ Tue, 30 Jun 2020 02:54:49: 17000000 INFO @ Tue, 30 Jun 2020 02:54:50: 22000000 INFO @ Tue, 30 Jun 2020 02:54:55: 28000000 INFO @ Tue, 30 Jun 2020 02:54:55: 18000000 INFO @ Tue, 30 Jun 2020 02:54:57: 23000000 INFO @ Tue, 30 Jun 2020 02:55:01: 29000000 INFO @ Tue, 30 Jun 2020 02:55:02: 19000000 INFO @ Tue, 30 Jun 2020 02:55:03: 24000000 INFO @ Tue, 30 Jun 2020 02:55:07: 30000000 INFO @ Tue, 30 Jun 2020 02:55:08: 20000000 INFO @ Tue, 30 Jun 2020 02:55:09: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:55:13: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 02:55:13: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 02:55:13: #1 total tags in treatment: 30825006 INFO @ Tue, 30 Jun 2020 02:55:13: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:55:13: #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 02:55:14: #1 tags after filtering in treatment: 30824948 INFO @ Tue, 30 Jun 2020 02:55:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:55:14: #1 finished! INFO @ Tue, 30 Jun 2020 02:55:14: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:55:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:55:14: 21000000 INFO @ Tue, 30 Jun 2020 02:55:16: 26000000 INFO @ Tue, 30 Jun 2020 02:55:16: #2 number of paired peaks: 185 WARNING @ Tue, 30 Jun 2020 02:55:16: 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 02:55:16: start model_add_line... INFO @ Tue, 30 Jun 2020 02:55:16: start X-correlation... INFO @ Tue, 30 Jun 2020 02:55:16: end of X-cor INFO @ Tue, 30 Jun 2020 02:55:16: #2 finished! INFO @ Tue, 30 Jun 2020 02:55:16: #2 predicted fragment length is 58 bps INFO @ Tue, 30 Jun 2020 02:55:16: #2 alternative fragment length(s) may be 2,58,580 bps INFO @ Tue, 30 Jun 2020 02:55:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4828020/SRX4828020.05_model.r WARNING @ Tue, 30 Jun 2020 02:55:16: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:55:16: #2 You may need to consider one of the other alternative d(s): 2,58,580 WARNING @ Tue, 30 Jun 2020 02:55:16: #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 02:55:16: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:55:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:55:20: 22000000 INFO @ Tue, 30 Jun 2020 02:55:22: 27000000 INFO @ Tue, 30 Jun 2020 02:55:26: 23000000 INFO @ Tue, 30 Jun 2020 02:55:28: 28000000 INFO @ Tue, 30 Jun 2020 02:55:33: 24000000 INFO @ Tue, 30 Jun 2020 02:55:34: 29000000 INFO @ Tue, 30 Jun 2020 02:55:39: 25000000 INFO @ Tue, 30 Jun 2020 02:55:41: 30000000 INFO @ Tue, 30 Jun 2020 02:55:45: 26000000 INFO @ Tue, 30 Jun 2020 02:55:46: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 02:55:46: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 02:55:46: #1 total tags in treatment: 30825006 INFO @ Tue, 30 Jun 2020 02:55:46: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:55:46: #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 02:55:47: #1 tags after filtering in treatment: 30824948 INFO @ Tue, 30 Jun 2020 02:55:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:55:47: #1 finished! INFO @ Tue, 30 Jun 2020 02:55:47: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:55:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:55:49: #2 number of paired peaks: 185 WARNING @ Tue, 30 Jun 2020 02:55:49: 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 02:55:49: start model_add_line... INFO @ Tue, 30 Jun 2020 02:55:49: start X-correlation... INFO @ Tue, 30 Jun 2020 02:55:49: end of X-cor INFO @ Tue, 30 Jun 2020 02:55:49: #2 finished! INFO @ Tue, 30 Jun 2020 02:55:49: #2 predicted fragment length is 58 bps INFO @ Tue, 30 Jun 2020 02:55:49: #2 alternative fragment length(s) may be 2,58,580 bps INFO @ Tue, 30 Jun 2020 02:55:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4828020/SRX4828020.10_model.r WARNING @ Tue, 30 Jun 2020 02:55:49: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:55:49: #2 You may need to consider one of the other alternative d(s): 2,58,580 WARNING @ Tue, 30 Jun 2020 02:55:49: #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 02:55:49: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:55:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:55:51: 27000000 INFO @ Tue, 30 Jun 2020 02:55:57: 28000000 INFO @ Tue, 30 Jun 2020 02:56:02: 29000000 INFO @ Tue, 30 Jun 2020 02:56:03: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:56:08: 30000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:56:13: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 02:56:13: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 02:56:13: #1 total tags in treatment: 30825006 INFO @ Tue, 30 Jun 2020 02:56:13: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:56:13: #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 02:56:14: #1 tags after filtering in treatment: 30824948 INFO @ Tue, 30 Jun 2020 02:56:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:56:14: #1 finished! INFO @ Tue, 30 Jun 2020 02:56:14: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:56:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:56:16: #2 number of paired peaks: 185 WARNING @ Tue, 30 Jun 2020 02:56:16: 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 02:56:16: start model_add_line... INFO @ Tue, 30 Jun 2020 02:56:16: start X-correlation... INFO @ Tue, 30 Jun 2020 02:56:16: end of X-cor INFO @ Tue, 30 Jun 2020 02:56:16: #2 finished! INFO @ Tue, 30 Jun 2020 02:56:16: #2 predicted fragment length is 58 bps INFO @ Tue, 30 Jun 2020 02:56:16: #2 alternative fragment length(s) may be 2,58,580 bps INFO @ Tue, 30 Jun 2020 02:56:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4828020/SRX4828020.20_model.r WARNING @ Tue, 30 Jun 2020 02:56:16: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:56:16: #2 You may need to consider one of the other alternative d(s): 2,58,580 WARNING @ Tue, 30 Jun 2020 02:56:16: #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 02:56:16: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:56:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:56:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4828020/SRX4828020.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:56:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4828020/SRX4828020.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:56:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4828020/SRX4828020.05_summits.bed INFO @ Tue, 30 Jun 2020 02:56:27: Done! pass1 - making usageList (625 chroms): 2 millis pass2 - checking and writing primary data (3302 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:56:37: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:57:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4828020/SRX4828020.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:57:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4828020/SRX4828020.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:57:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4828020/SRX4828020.10_summits.bed INFO @ Tue, 30 Jun 2020 02:57:00: Done! pass1 - making usageList (449 chroms): 1 millis pass2 - checking and writing primary data (1510 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:57:05: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:57:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4828020/SRX4828020.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:57:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4828020/SRX4828020.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:57:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4828020/SRX4828020.20_summits.bed INFO @ Tue, 30 Jun 2020 02:57:29: Done! pass1 - making usageList (228 chroms): 1 millis pass2 - checking and writing primary data (600 records, 4 fields): 9 millis CompletedMACS2peakCalling