Job ID = 6529239 SRX = SRX1084162 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: 00:04:51 21759793 reads; of these: 21759793 (100.00%) were unpaired; of these: 4270642 (19.63%) aligned 0 times 13954686 (64.13%) aligned exactly 1 time 3534465 (16.24%) aligned >1 times 80.37% overall alignment rate Time searching: 00:04:51 Overall time: 00:04:51 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] 1710517 / 17489151 = 0.0978 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 01:44:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1084162/SRX1084162.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1084162/SRX1084162.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1084162/SRX1084162.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1084162/SRX1084162.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 01:44:23: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:44:23: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:44:28: 1000000 INFO @ Tue, 30 Jun 2020 01:44:33: 2000000 INFO @ Tue, 30 Jun 2020 01:44:38: 3000000 INFO @ Tue, 30 Jun 2020 01:44:44: 4000000 INFO @ Tue, 30 Jun 2020 01:44:49: 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 01:44:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1084162/SRX1084162.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1084162/SRX1084162.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1084162/SRX1084162.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1084162/SRX1084162.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 01:44:53: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:44:53: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:44:55: 6000000 INFO @ Tue, 30 Jun 2020 01:45:00: 1000000 INFO @ Tue, 30 Jun 2020 01:45:01: 7000000 INFO @ Tue, 30 Jun 2020 01:45:06: 2000000 INFO @ Tue, 30 Jun 2020 01:45:07: 8000000 INFO @ Tue, 30 Jun 2020 01:45:13: 3000000 INFO @ Tue, 30 Jun 2020 01:45:13: 9000000 INFO @ Tue, 30 Jun 2020 01:45:20: 10000000 INFO @ Tue, 30 Jun 2020 01:45:20: 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 01:45:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1084162/SRX1084162.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1084162/SRX1084162.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1084162/SRX1084162.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1084162/SRX1084162.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 01:45:23: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:45:23: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:45:26: 11000000 INFO @ Tue, 30 Jun 2020 01:45:27: 5000000 INFO @ Tue, 30 Jun 2020 01:45:30: 1000000 INFO @ Tue, 30 Jun 2020 01:45:32: 12000000 INFO @ Tue, 30 Jun 2020 01:45:33: 6000000 INFO @ Tue, 30 Jun 2020 01:45:37: 2000000 INFO @ Tue, 30 Jun 2020 01:45:39: 13000000 INFO @ Tue, 30 Jun 2020 01:45:40: 7000000 INFO @ Tue, 30 Jun 2020 01:45:44: 3000000 INFO @ Tue, 30 Jun 2020 01:45:45: 14000000 INFO @ Tue, 30 Jun 2020 01:45:47: 8000000 INFO @ Tue, 30 Jun 2020 01:45:50: 4000000 INFO @ Tue, 30 Jun 2020 01:45:51: 15000000 INFO @ Tue, 30 Jun 2020 01:45:53: 9000000 INFO @ Tue, 30 Jun 2020 01:45:57: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 01:45:57: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 01:45:57: #1 total tags in treatment: 15778634 INFO @ Tue, 30 Jun 2020 01:45:57: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:45:57: #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 01:45:57: #1 tags after filtering in treatment: 15778570 INFO @ Tue, 30 Jun 2020 01:45:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:45:57: #1 finished! INFO @ Tue, 30 Jun 2020 01:45:57: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:45:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:45:57: 5000000 INFO @ Tue, 30 Jun 2020 01:45:58: #2 number of paired peaks: 239 WARNING @ Tue, 30 Jun 2020 01:45:58: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Tue, 30 Jun 2020 01:45:58: start model_add_line... INFO @ Tue, 30 Jun 2020 01:45:58: start X-correlation... INFO @ Tue, 30 Jun 2020 01:45:58: end of X-cor INFO @ Tue, 30 Jun 2020 01:45:58: #2 finished! INFO @ Tue, 30 Jun 2020 01:45:58: #2 predicted fragment length is 49 bps INFO @ Tue, 30 Jun 2020 01:45:58: #2 alternative fragment length(s) may be 4,49 bps INFO @ Tue, 30 Jun 2020 01:45:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1084162/SRX1084162.05_model.r WARNING @ Tue, 30 Jun 2020 01:45:58: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:45:58: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Tue, 30 Jun 2020 01:45:58: #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 01:45:58: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:45:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:46:00: 10000000 INFO @ Tue, 30 Jun 2020 01:46:04: 6000000 INFO @ Tue, 30 Jun 2020 01:46:07: 11000000 INFO @ Tue, 30 Jun 2020 01:46:11: 7000000 INFO @ Tue, 30 Jun 2020 01:46:13: 12000000 INFO @ Tue, 30 Jun 2020 01:46:18: 8000000 INFO @ Tue, 30 Jun 2020 01:46:21: 13000000 INFO @ Tue, 30 Jun 2020 01:46:25: 9000000 INFO @ Tue, 30 Jun 2020 01:46:27: 14000000 INFO @ Tue, 30 Jun 2020 01:46:29: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:46:32: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:46:34: 15000000 INFO @ Tue, 30 Jun 2020 01:46:38: 11000000 INFO @ Tue, 30 Jun 2020 01:46:39: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 01:46:39: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 01:46:39: #1 total tags in treatment: 15778634 INFO @ Tue, 30 Jun 2020 01:46:39: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:46:39: #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 01:46:40: #1 tags after filtering in treatment: 15778570 INFO @ Tue, 30 Jun 2020 01:46:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:46:40: #1 finished! INFO @ Tue, 30 Jun 2020 01:46:40: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:46:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:46:41: #2 number of paired peaks: 239 WARNING @ Tue, 30 Jun 2020 01:46:41: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Tue, 30 Jun 2020 01:46:41: start model_add_line... INFO @ Tue, 30 Jun 2020 01:46:41: start X-correlation... INFO @ Tue, 30 Jun 2020 01:46:41: end of X-cor INFO @ Tue, 30 Jun 2020 01:46:41: #2 finished! INFO @ Tue, 30 Jun 2020 01:46:41: #2 predicted fragment length is 49 bps INFO @ Tue, 30 Jun 2020 01:46:41: #2 alternative fragment length(s) may be 4,49 bps INFO @ Tue, 30 Jun 2020 01:46:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1084162/SRX1084162.10_model.r WARNING @ Tue, 30 Jun 2020 01:46:41: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:46:41: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Tue, 30 Jun 2020 01:46:41: #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 01:46:41: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:46:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:46:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1084162/SRX1084162.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:46:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1084162/SRX1084162.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:46:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1084162/SRX1084162.05_summits.bed INFO @ Tue, 30 Jun 2020 01:46:44: Done! pass1 - making usageList (550 chroms): 2 millis pass2 - checking and writing primary data (3875 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:46:45: 12000000 INFO @ Tue, 30 Jun 2020 01:46:52: 13000000 INFO @ Tue, 30 Jun 2020 01:46:58: 14000000 INFO @ Tue, 30 Jun 2020 01:47:04: 15000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:47:10: #1 tag size is determined as 49 bps INFO @ Tue, 30 Jun 2020 01:47:10: #1 tag size = 49 INFO @ Tue, 30 Jun 2020 01:47:10: #1 total tags in treatment: 15778634 INFO @ Tue, 30 Jun 2020 01:47:10: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:47:10: #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 01:47:10: #1 tags after filtering in treatment: 15778570 INFO @ Tue, 30 Jun 2020 01:47:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:47:10: #1 finished! INFO @ Tue, 30 Jun 2020 01:47:10: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:47:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:47:10: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:47:11: #2 number of paired peaks: 239 WARNING @ Tue, 30 Jun 2020 01:47:11: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Tue, 30 Jun 2020 01:47:11: start model_add_line... INFO @ Tue, 30 Jun 2020 01:47:11: start X-correlation... INFO @ Tue, 30 Jun 2020 01:47:11: end of X-cor INFO @ Tue, 30 Jun 2020 01:47:11: #2 finished! INFO @ Tue, 30 Jun 2020 01:47:11: #2 predicted fragment length is 49 bps INFO @ Tue, 30 Jun 2020 01:47:11: #2 alternative fragment length(s) may be 4,49 bps INFO @ Tue, 30 Jun 2020 01:47:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1084162/SRX1084162.20_model.r WARNING @ Tue, 30 Jun 2020 01:47:11: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:47:11: #2 You may need to consider one of the other alternative d(s): 4,49 WARNING @ Tue, 30 Jun 2020 01:47:11: #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 01:47:11: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:47:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:47:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1084162/SRX1084162.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:47:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1084162/SRX1084162.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:47:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1084162/SRX1084162.10_summits.bed INFO @ Tue, 30 Jun 2020 01:47:25: Done! pass1 - making usageList (413 chroms): 1 millis pass2 - checking and writing primary data (1645 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:47:40: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:47:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1084162/SRX1084162.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:47:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1084162/SRX1084162.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:47:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1084162/SRX1084162.20_summits.bed INFO @ Tue, 30 Jun 2020 01:47:55: Done! pass1 - making usageList (156 chroms): 1 millis pass2 - checking and writing primary data (311 records, 4 fields): 5 millis CompletedMACS2peakCalling