Job ID = 6529988 SRX = SRX5775908 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: 00:10:52 27099927 reads; of these: 27099927 (100.00%) were unpaired; of these: 722081 (2.66%) aligned 0 times 19345656 (71.39%) aligned exactly 1 time 7032190 (25.95%) aligned >1 times 97.34% overall alignment rate Time searching: 00:10:52 Overall time: 00:10:52 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] 9444746 / 26377846 = 0.3581 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 03:25:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775908/SRX5775908.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775908/SRX5775908.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775908/SRX5775908.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775908/SRX5775908.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 03:25:00: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:25:00: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:25:05: 1000000 INFO @ Tue, 30 Jun 2020 03:25:10: 2000000 INFO @ Tue, 30 Jun 2020 03:25:15: 3000000 INFO @ Tue, 30 Jun 2020 03:25:20: 4000000 INFO @ Tue, 30 Jun 2020 03:25:25: 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 03:25:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775908/SRX5775908.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775908/SRX5775908.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775908/SRX5775908.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775908/SRX5775908.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 03:25:30: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:25:30: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:25:30: 6000000 INFO @ Tue, 30 Jun 2020 03:25:35: 1000000 INFO @ Tue, 30 Jun 2020 03:25:36: 7000000 INFO @ Tue, 30 Jun 2020 03:25:41: 2000000 INFO @ Tue, 30 Jun 2020 03:25:41: 8000000 INFO @ Tue, 30 Jun 2020 03:25:46: 3000000 INFO @ Tue, 30 Jun 2020 03:25:46: 9000000 INFO @ Tue, 30 Jun 2020 03:25:51: 4000000 INFO @ Tue, 30 Jun 2020 03:25:52: 10000000 INFO @ Tue, 30 Jun 2020 03:25:56: 5000000 INFO @ Tue, 30 Jun 2020 03:25:57: 11000000 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 03:26:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775908/SRX5775908.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775908/SRX5775908.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775908/SRX5775908.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775908/SRX5775908.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 03:26:00: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:26:00: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:26:01: 6000000 INFO @ Tue, 30 Jun 2020 03:26:02: 12000000 INFO @ Tue, 30 Jun 2020 03:26:06: 1000000 INFO @ Tue, 30 Jun 2020 03:26:07: 7000000 INFO @ Tue, 30 Jun 2020 03:26:08: 13000000 INFO @ Tue, 30 Jun 2020 03:26:12: 2000000 INFO @ Tue, 30 Jun 2020 03:26:12: 8000000 INFO @ Tue, 30 Jun 2020 03:26:14: 14000000 INFO @ Tue, 30 Jun 2020 03:26:17: 3000000 INFO @ Tue, 30 Jun 2020 03:26:17: 9000000 INFO @ Tue, 30 Jun 2020 03:26:19: 15000000 INFO @ Tue, 30 Jun 2020 03:26:23: 10000000 INFO @ Tue, 30 Jun 2020 03:26:23: 4000000 INFO @ Tue, 30 Jun 2020 03:26:25: 16000000 INFO @ Tue, 30 Jun 2020 03:26:28: 11000000 INFO @ Tue, 30 Jun 2020 03:26:29: 5000000 INFO @ Tue, 30 Jun 2020 03:26:30: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 03:26:30: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 03:26:30: #1 total tags in treatment: 16933100 INFO @ Tue, 30 Jun 2020 03:26:30: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:26:30: #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 03:26:31: #1 tags after filtering in treatment: 16933100 INFO @ Tue, 30 Jun 2020 03:26:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:26:31: #1 finished! INFO @ Tue, 30 Jun 2020 03:26:31: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:26:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:26:32: #2 number of paired peaks: 668 WARNING @ Tue, 30 Jun 2020 03:26:32: Fewer paired peaks (668) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 668 pairs to build model! INFO @ Tue, 30 Jun 2020 03:26:32: start model_add_line... INFO @ Tue, 30 Jun 2020 03:26:32: start X-correlation... INFO @ Tue, 30 Jun 2020 03:26:32: end of X-cor INFO @ Tue, 30 Jun 2020 03:26:32: #2 finished! INFO @ Tue, 30 Jun 2020 03:26:32: #2 predicted fragment length is 68 bps INFO @ Tue, 30 Jun 2020 03:26:32: #2 alternative fragment length(s) may be 3,68 bps INFO @ Tue, 30 Jun 2020 03:26:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775908/SRX5775908.05_model.r WARNING @ Tue, 30 Jun 2020 03:26:32: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:26:32: #2 You may need to consider one of the other alternative d(s): 3,68 WARNING @ Tue, 30 Jun 2020 03:26:32: #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 03:26:32: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:26:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:26:34: 12000000 INFO @ Tue, 30 Jun 2020 03:26:36: 6000000 INFO @ Tue, 30 Jun 2020 03:26:39: 13000000 INFO @ Tue, 30 Jun 2020 03:26:43: 7000000 INFO @ Tue, 30 Jun 2020 03:26:45: 14000000 INFO @ Tue, 30 Jun 2020 03:26:50: 8000000 INFO @ Tue, 30 Jun 2020 03:26:51: 15000000 INFO @ Tue, 30 Jun 2020 03:26:56: 16000000 INFO @ Tue, 30 Jun 2020 03:26:58: 9000000 INFO @ Tue, 30 Jun 2020 03:27:02: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 03:27:02: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 03:27:02: #1 total tags in treatment: 16933100 INFO @ Tue, 30 Jun 2020 03:27:02: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:27:02: #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 03:27:02: #1 tags after filtering in treatment: 16933100 INFO @ Tue, 30 Jun 2020 03:27:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:27:02: #1 finished! INFO @ Tue, 30 Jun 2020 03:27:02: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:27:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:27:03: #2 number of paired peaks: 668 WARNING @ Tue, 30 Jun 2020 03:27:03: Fewer paired peaks (668) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 668 pairs to build model! INFO @ Tue, 30 Jun 2020 03:27:03: start model_add_line... INFO @ Tue, 30 Jun 2020 03:27:04: start X-correlation... INFO @ Tue, 30 Jun 2020 03:27:04: end of X-cor INFO @ Tue, 30 Jun 2020 03:27:04: #2 finished! INFO @ Tue, 30 Jun 2020 03:27:04: #2 predicted fragment length is 68 bps INFO @ Tue, 30 Jun 2020 03:27:04: #2 alternative fragment length(s) may be 3,68 bps INFO @ Tue, 30 Jun 2020 03:27:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775908/SRX5775908.10_model.r WARNING @ Tue, 30 Jun 2020 03:27:04: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:27:04: #2 You may need to consider one of the other alternative d(s): 3,68 WARNING @ Tue, 30 Jun 2020 03:27:04: #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 03:27:04: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:27:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:27:06: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:27:06: 10000000 INFO @ Tue, 30 Jun 2020 03:27:13: 11000000 INFO @ Tue, 30 Jun 2020 03:27:19: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:27:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775908/SRX5775908.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:27:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775908/SRX5775908.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:27:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775908/SRX5775908.05_summits.bed INFO @ Tue, 30 Jun 2020 03:27:21: Done! pass1 - making usageList (815 chroms): 1 millis pass2 - checking and writing primary data (2765 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:27:25: 13000000 INFO @ Tue, 30 Jun 2020 03:27:31: 14000000 INFO @ Tue, 30 Jun 2020 03:27:36: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:27:37: 15000000 INFO @ Tue, 30 Jun 2020 03:27:43: 16000000 INFO @ Tue, 30 Jun 2020 03:27:50: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 03:27:50: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 03:27:50: #1 total tags in treatment: 16933100 INFO @ Tue, 30 Jun 2020 03:27:50: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:27:50: #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 03:27:50: #1 tags after filtering in treatment: 16933100 INFO @ Tue, 30 Jun 2020 03:27:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:27:50: #1 finished! INFO @ Tue, 30 Jun 2020 03:27:50: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:27:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:27:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775908/SRX5775908.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:27:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775908/SRX5775908.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:27:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775908/SRX5775908.10_summits.bed INFO @ Tue, 30 Jun 2020 03:27:51: Done! INFO @ Tue, 30 Jun 2020 03:27:51: #2 number of paired peaks: 668 WARNING @ Tue, 30 Jun 2020 03:27:51: Fewer paired peaks (668) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 668 pairs to build model! INFO @ Tue, 30 Jun 2020 03:27:51: start model_add_line... INFO @ Tue, 30 Jun 2020 03:27:51: start X-correlation... INFO @ Tue, 30 Jun 2020 03:27:51: end of X-cor INFO @ Tue, 30 Jun 2020 03:27:51: #2 finished! INFO @ Tue, 30 Jun 2020 03:27:51: #2 predicted fragment length is 68 bps INFO @ Tue, 30 Jun 2020 03:27:51: #2 alternative fragment length(s) may be 3,68 bps INFO @ Tue, 30 Jun 2020 03:27:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775908/SRX5775908.20_model.r WARNING @ Tue, 30 Jun 2020 03:27:51: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:27:51: #2 You may need to consider one of the other alternative d(s): 3,68 WARNING @ Tue, 30 Jun 2020 03:27:51: #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 03:27:51: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:27:51: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (684 chroms): 1 millis pass2 - checking and writing primary data (2024 records, 4 fields): 18 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:28:25: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:28:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775908/SRX5775908.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:28:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775908/SRX5775908.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:28:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775908/SRX5775908.20_summits.bed INFO @ Tue, 30 Jun 2020 03:28:40: Done! pass1 - making usageList (513 chroms): 1 millis pass2 - checking and writing primary data (1300 records, 4 fields): 15 millis CompletedMACS2peakCalling