Job ID = 6529485 SRX = SRX287777 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: 00:04:43 17761171 reads; of these: 17761171 (100.00%) were unpaired; of these: 1061844 (5.98%) aligned 0 times 12962584 (72.98%) aligned exactly 1 time 3736743 (21.04%) aligned >1 times 94.02% overall alignment rate Time searching: 00:04:43 Overall time: 00:04:43 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 8 files... [bam_rmdupse_core] 1638628 / 16699327 = 0.0981 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 02:18:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287777/SRX287777.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287777/SRX287777.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287777/SRX287777.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287777/SRX287777.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 02:18:32: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:18:32: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:18:38: 1000000 INFO @ Tue, 30 Jun 2020 02:18:43: 2000000 INFO @ Tue, 30 Jun 2020 02:18:48: 3000000 INFO @ Tue, 30 Jun 2020 02:18:54: 4000000 INFO @ Tue, 30 Jun 2020 02:18:59: 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 02:19:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287777/SRX287777.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287777/SRX287777.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287777/SRX287777.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287777/SRX287777.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 02:19:02: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:19:02: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:19:05: 6000000 INFO @ Tue, 30 Jun 2020 02:19:08: 1000000 INFO @ Tue, 30 Jun 2020 02:19:10: 7000000 INFO @ Tue, 30 Jun 2020 02:19:14: 2000000 INFO @ Tue, 30 Jun 2020 02:19:16: 8000000 INFO @ Tue, 30 Jun 2020 02:19:20: 3000000 INFO @ Tue, 30 Jun 2020 02:19:22: 9000000 INFO @ Tue, 30 Jun 2020 02:19:26: 4000000 INFO @ Tue, 30 Jun 2020 02:19:28: 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 02:19:32: 5000000 INFO @ Tue, 30 Jun 2020 02:19:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287777/SRX287777.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287777/SRX287777.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287777/SRX287777.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287777/SRX287777.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 02:19:33: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:19:33: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:19:34: 11000000 INFO @ Tue, 30 Jun 2020 02:19:38: 6000000 INFO @ Tue, 30 Jun 2020 02:19:40: 1000000 INFO @ Tue, 30 Jun 2020 02:19:41: 12000000 INFO @ Tue, 30 Jun 2020 02:19:44: 7000000 INFO @ Tue, 30 Jun 2020 02:19:46: 2000000 INFO @ Tue, 30 Jun 2020 02:19:49: 13000000 INFO @ Tue, 30 Jun 2020 02:19:51: 8000000 INFO @ Tue, 30 Jun 2020 02:19:52: 3000000 INFO @ Tue, 30 Jun 2020 02:19:55: 14000000 INFO @ Tue, 30 Jun 2020 02:19:58: 9000000 INFO @ Tue, 30 Jun 2020 02:19:59: 4000000 INFO @ Tue, 30 Jun 2020 02:20:02: 15000000 INFO @ Tue, 30 Jun 2020 02:20:03: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:20:03: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:20:03: #1 total tags in treatment: 15060699 INFO @ Tue, 30 Jun 2020 02:20:03: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:20:03: #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 02:20:03: #1 tags after filtering in treatment: 15060699 INFO @ Tue, 30 Jun 2020 02:20:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:20:03: #1 finished! INFO @ Tue, 30 Jun 2020 02:20:03: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:20:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:20:04: 10000000 INFO @ Tue, 30 Jun 2020 02:20:05: #2 number of paired peaks: 318 WARNING @ Tue, 30 Jun 2020 02:20:05: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Tue, 30 Jun 2020 02:20:05: start model_add_line... INFO @ Tue, 30 Jun 2020 02:20:05: start X-correlation... INFO @ Tue, 30 Jun 2020 02:20:05: end of X-cor INFO @ Tue, 30 Jun 2020 02:20:05: #2 finished! INFO @ Tue, 30 Jun 2020 02:20:05: #2 predicted fragment length is 35 bps INFO @ Tue, 30 Jun 2020 02:20:05: #2 alternative fragment length(s) may be 3,35,564 bps INFO @ Tue, 30 Jun 2020 02:20:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287777/SRX287777.05_model.r INFO @ Tue, 30 Jun 2020 02:20:05: 5000000 WARNING @ Tue, 30 Jun 2020 02:20:05: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:20:05: #2 You may need to consider one of the other alternative d(s): 3,35,564 WARNING @ Tue, 30 Jun 2020 02:20:05: #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 02:20:05: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:20:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:20:10: 11000000 INFO @ Tue, 30 Jun 2020 02:20:11: 6000000 INFO @ Tue, 30 Jun 2020 02:20:16: 12000000 INFO @ Tue, 30 Jun 2020 02:20:17: 7000000 INFO @ Tue, 30 Jun 2020 02:20:23: 8000000 INFO @ Tue, 30 Jun 2020 02:20:23: 13000000 INFO @ Tue, 30 Jun 2020 02:20:29: 9000000 INFO @ Tue, 30 Jun 2020 02:20:30: 14000000 INFO @ Tue, 30 Jun 2020 02:20:31: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:20:35: 10000000 INFO @ Tue, 30 Jun 2020 02:20:36: 15000000 INFO @ Tue, 30 Jun 2020 02:20:37: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:20:37: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:20:37: #1 total tags in treatment: 15060699 INFO @ Tue, 30 Jun 2020 02:20:37: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:20:37: #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 02:20:37: #1 tags after filtering in treatment: 15060699 INFO @ Tue, 30 Jun 2020 02:20:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:20:37: #1 finished! INFO @ Tue, 30 Jun 2020 02:20:37: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:20:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:20:39: #2 number of paired peaks: 318 WARNING @ Tue, 30 Jun 2020 02:20:39: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Tue, 30 Jun 2020 02:20:39: start model_add_line... INFO @ Tue, 30 Jun 2020 02:20:39: start X-correlation... INFO @ Tue, 30 Jun 2020 02:20:39: end of X-cor INFO @ Tue, 30 Jun 2020 02:20:39: #2 finished! INFO @ Tue, 30 Jun 2020 02:20:39: #2 predicted fragment length is 35 bps INFO @ Tue, 30 Jun 2020 02:20:39: #2 alternative fragment length(s) may be 3,35,564 bps INFO @ Tue, 30 Jun 2020 02:20:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287777/SRX287777.10_model.r WARNING @ Tue, 30 Jun 2020 02:20:39: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:20:39: #2 You may need to consider one of the other alternative d(s): 3,35,564 WARNING @ Tue, 30 Jun 2020 02:20:39: #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 02:20:39: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:20:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:20:40: 11000000 INFO @ Tue, 30 Jun 2020 02:20:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287777/SRX287777.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:20:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287777/SRX287777.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:20:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287777/SRX287777.05_summits.bed INFO @ Tue, 30 Jun 2020 02:20:45: Done! pass1 - making usageList (513 chroms): 2 millis pass2 - checking and writing primary data (2158 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:20:46: 12000000 INFO @ Tue, 30 Jun 2020 02:20:52: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:20:58: 14000000 INFO @ Tue, 30 Jun 2020 02:21:04: 15000000 INFO @ Tue, 30 Jun 2020 02:21:04: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:21:04: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:21:04: #1 total tags in treatment: 15060699 INFO @ Tue, 30 Jun 2020 02:21:04: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:21:04: #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 02:21:05: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:21:05: #1 tags after filtering in treatment: 15060699 INFO @ Tue, 30 Jun 2020 02:21:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:21:05: #1 finished! INFO @ Tue, 30 Jun 2020 02:21:05: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:21:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:21:06: #2 number of paired peaks: 318 WARNING @ Tue, 30 Jun 2020 02:21:06: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Tue, 30 Jun 2020 02:21:06: start model_add_line... INFO @ Tue, 30 Jun 2020 02:21:06: start X-correlation... INFO @ Tue, 30 Jun 2020 02:21:06: end of X-cor INFO @ Tue, 30 Jun 2020 02:21:06: #2 finished! INFO @ Tue, 30 Jun 2020 02:21:06: #2 predicted fragment length is 35 bps INFO @ Tue, 30 Jun 2020 02:21:06: #2 alternative fragment length(s) may be 3,35,564 bps INFO @ Tue, 30 Jun 2020 02:21:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287777/SRX287777.20_model.r WARNING @ Tue, 30 Jun 2020 02:21:06: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:21:06: #2 You may need to consider one of the other alternative d(s): 3,35,564 WARNING @ Tue, 30 Jun 2020 02:21:06: #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 02:21:06: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:21:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:21:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287777/SRX287777.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:21:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287777/SRX287777.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:21:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287777/SRX287777.10_summits.bed INFO @ Tue, 30 Jun 2020 02:21:18: Done! pass1 - making usageList (437 chroms): 2 millis pass2 - checking and writing primary data (1535 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:21:32: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:21:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287777/SRX287777.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:21:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287777/SRX287777.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:21:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287777/SRX287777.20_summits.bed INFO @ Tue, 30 Jun 2020 02:21:45: Done! pass1 - making usageList (206 chroms): 1 millis pass2 - checking and writing primary data (396 records, 4 fields): 12 millis CompletedMACS2peakCalling