Job ID = 6529808 SRX = SRX4933895 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: 00:09:18 30600201 reads; of these: 30600201 (100.00%) were unpaired; of these: 1392248 (4.55%) aligned 0 times 21756431 (71.10%) aligned exactly 1 time 7451522 (24.35%) aligned >1 times 95.45% overall alignment rate Time searching: 00:09:18 Overall time: 00:09:18 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 12 files... [bam_rmdupse_core] 7314805 / 29207953 = 0.2504 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 03:14:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933895/SRX4933895.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933895/SRX4933895.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933895/SRX4933895.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933895/SRX4933895.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 03:14:42: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:14:42: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:14:50: 1000000 INFO @ Tue, 30 Jun 2020 03:14:57: 2000000 INFO @ Tue, 30 Jun 2020 03:15:05: 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 03:15:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933895/SRX4933895.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933895/SRX4933895.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933895/SRX4933895.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933895/SRX4933895.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 03:15:11: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:15:11: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:15:12: 4000000 INFO @ Tue, 30 Jun 2020 03:15:19: 1000000 INFO @ Tue, 30 Jun 2020 03:15:20: 5000000 INFO @ Tue, 30 Jun 2020 03:15:27: 2000000 INFO @ Tue, 30 Jun 2020 03:15:28: 6000000 INFO @ Tue, 30 Jun 2020 03:15:35: 3000000 INFO @ Tue, 30 Jun 2020 03:15:36: 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 03:15:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4933895/SRX4933895.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4933895/SRX4933895.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4933895/SRX4933895.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4933895/SRX4933895.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 03:15:41: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:15:41: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:15:43: 4000000 INFO @ Tue, 30 Jun 2020 03:15:44: 8000000 INFO @ Tue, 30 Jun 2020 03:15:49: 1000000 INFO @ Tue, 30 Jun 2020 03:15:51: 5000000 INFO @ Tue, 30 Jun 2020 03:15:52: 9000000 INFO @ Tue, 30 Jun 2020 03:15:57: 2000000 INFO @ Tue, 30 Jun 2020 03:15:58: 6000000 INFO @ Tue, 30 Jun 2020 03:16:00: 10000000 INFO @ Tue, 30 Jun 2020 03:16:05: 3000000 INFO @ Tue, 30 Jun 2020 03:16:06: 7000000 INFO @ Tue, 30 Jun 2020 03:16:08: 11000000 INFO @ Tue, 30 Jun 2020 03:16:13: 4000000 INFO @ Tue, 30 Jun 2020 03:16:14: 8000000 INFO @ Tue, 30 Jun 2020 03:16:16: 12000000 INFO @ Tue, 30 Jun 2020 03:16:21: 5000000 INFO @ Tue, 30 Jun 2020 03:16:22: 9000000 INFO @ Tue, 30 Jun 2020 03:16:24: 13000000 INFO @ Tue, 30 Jun 2020 03:16:29: 6000000 INFO @ Tue, 30 Jun 2020 03:16:30: 10000000 INFO @ Tue, 30 Jun 2020 03:16:32: 14000000 INFO @ Tue, 30 Jun 2020 03:16:37: 7000000 INFO @ Tue, 30 Jun 2020 03:16:38: 11000000 INFO @ Tue, 30 Jun 2020 03:16:40: 15000000 INFO @ Tue, 30 Jun 2020 03:16:45: 8000000 INFO @ Tue, 30 Jun 2020 03:16:46: 12000000 INFO @ Tue, 30 Jun 2020 03:16:48: 16000000 INFO @ Tue, 30 Jun 2020 03:16:53: 9000000 INFO @ Tue, 30 Jun 2020 03:16:54: 13000000 INFO @ Tue, 30 Jun 2020 03:16:56: 17000000 INFO @ Tue, 30 Jun 2020 03:17:02: 10000000 INFO @ Tue, 30 Jun 2020 03:17:02: 14000000 INFO @ Tue, 30 Jun 2020 03:17:05: 18000000 INFO @ Tue, 30 Jun 2020 03:17:10: 11000000 INFO @ Tue, 30 Jun 2020 03:17:10: 15000000 INFO @ Tue, 30 Jun 2020 03:17:13: 19000000 INFO @ Tue, 30 Jun 2020 03:17:18: 16000000 INFO @ Tue, 30 Jun 2020 03:17:18: 12000000 INFO @ Tue, 30 Jun 2020 03:17:21: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:17:26: 17000000 INFO @ Tue, 30 Jun 2020 03:17:26: 13000000 INFO @ Tue, 30 Jun 2020 03:17:29: 21000000 INFO @ Tue, 30 Jun 2020 03:17:35: 18000000 INFO @ Tue, 30 Jun 2020 03:17:35: 14000000 INFO @ Tue, 30 Jun 2020 03:17:37: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:17:37: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:17:37: #1 total tags in treatment: 21893148 INFO @ Tue, 30 Jun 2020 03:17:37: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:17:37: #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 03:17:37: #1 tags after filtering in treatment: 21893148 INFO @ Tue, 30 Jun 2020 03:17:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:17:37: #1 finished! INFO @ Tue, 30 Jun 2020 03:17:37: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:17:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:17:39: #2 number of paired peaks: 311 WARNING @ Tue, 30 Jun 2020 03:17:39: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Tue, 30 Jun 2020 03:17:39: start model_add_line... INFO @ Tue, 30 Jun 2020 03:17:39: start X-correlation... INFO @ Tue, 30 Jun 2020 03:17:39: end of X-cor INFO @ Tue, 30 Jun 2020 03:17:39: #2 finished! INFO @ Tue, 30 Jun 2020 03:17:39: #2 predicted fragment length is 48 bps INFO @ Tue, 30 Jun 2020 03:17:39: #2 alternative fragment length(s) may be 2,48 bps INFO @ Tue, 30 Jun 2020 03:17:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933895/SRX4933895.05_model.r WARNING @ Tue, 30 Jun 2020 03:17:39: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:17:39: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Tue, 30 Jun 2020 03:17:39: #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 03:17:39: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:17:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:17:43: 19000000 INFO @ Tue, 30 Jun 2020 03:17:43: 15000000 INFO @ Tue, 30 Jun 2020 03:17:51: 16000000 INFO @ Tue, 30 Jun 2020 03:17:51: 20000000 INFO @ Tue, 30 Jun 2020 03:17:59: 17000000 INFO @ Tue, 30 Jun 2020 03:17:59: 21000000 INFO @ Tue, 30 Jun 2020 03:18:07: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:18:07: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:18:07: #1 total tags in treatment: 21893148 INFO @ Tue, 30 Jun 2020 03:18:07: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:18:07: #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 03:18:07: 18000000 INFO @ Tue, 30 Jun 2020 03:18:08: #1 tags after filtering in treatment: 21893148 INFO @ Tue, 30 Jun 2020 03:18:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:18:08: #1 finished! INFO @ Tue, 30 Jun 2020 03:18:08: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:18:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:18:09: #2 number of paired peaks: 311 WARNING @ Tue, 30 Jun 2020 03:18:09: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Tue, 30 Jun 2020 03:18:09: start model_add_line... INFO @ Tue, 30 Jun 2020 03:18:09: start X-correlation... INFO @ Tue, 30 Jun 2020 03:18:09: end of X-cor INFO @ Tue, 30 Jun 2020 03:18:09: #2 finished! INFO @ Tue, 30 Jun 2020 03:18:09: #2 predicted fragment length is 48 bps INFO @ Tue, 30 Jun 2020 03:18:09: #2 alternative fragment length(s) may be 2,48 bps INFO @ Tue, 30 Jun 2020 03:18:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933895/SRX4933895.10_model.r WARNING @ Tue, 30 Jun 2020 03:18:09: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:18:09: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Tue, 30 Jun 2020 03:18:09: #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 03:18:09: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:18:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:18:15: 19000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:18:21: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:18:23: 20000000 INFO @ Tue, 30 Jun 2020 03:18:31: 21000000 INFO @ Tue, 30 Jun 2020 03:18:38: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 03:18:38: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 03:18:38: #1 total tags in treatment: 21893148 INFO @ Tue, 30 Jun 2020 03:18:38: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:18:38: #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 03:18:38: #1 tags after filtering in treatment: 21893148 INFO @ Tue, 30 Jun 2020 03:18:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:18:38: #1 finished! INFO @ Tue, 30 Jun 2020 03:18:38: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:18:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:18:40: #2 number of paired peaks: 311 WARNING @ Tue, 30 Jun 2020 03:18:40: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Tue, 30 Jun 2020 03:18:40: start model_add_line... INFO @ Tue, 30 Jun 2020 03:18:40: start X-correlation... INFO @ Tue, 30 Jun 2020 03:18:40: end of X-cor INFO @ Tue, 30 Jun 2020 03:18:40: #2 finished! INFO @ Tue, 30 Jun 2020 03:18:40: #2 predicted fragment length is 48 bps INFO @ Tue, 30 Jun 2020 03:18:40: #2 alternative fragment length(s) may be 2,48 bps INFO @ Tue, 30 Jun 2020 03:18:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4933895/SRX4933895.20_model.r WARNING @ Tue, 30 Jun 2020 03:18:40: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:18:40: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Tue, 30 Jun 2020 03:18:40: #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 03:18:40: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:18:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:18:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933895/SRX4933895.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:18:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933895/SRX4933895.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:18:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933895/SRX4933895.05_summits.bed INFO @ Tue, 30 Jun 2020 03:18:42: Done! pass1 - making usageList (716 chroms): 2 millis pass2 - checking and writing primary data (3217 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:18:50: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:19:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933895/SRX4933895.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:19:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933895/SRX4933895.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:19:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933895/SRX4933895.10_summits.bed INFO @ Tue, 30 Jun 2020 03:19:10: Done! pass1 - making usageList (611 chroms): 2 millis pass2 - checking and writing primary data (2463 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:19:22: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:19:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4933895/SRX4933895.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:19:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4933895/SRX4933895.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:19:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4933895/SRX4933895.20_summits.bed INFO @ Tue, 30 Jun 2020 03:19:41: Done! pass1 - making usageList (388 chroms): 1 millis pass2 - checking and writing primary data (871 records, 4 fields): 12 millis CompletedMACS2peakCalling