Job ID = 6529675 SRX = SRX3981649 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: 00:10:07 35614225 reads; of these: 35614225 (100.00%) were unpaired; of these: 1489346 (4.18%) aligned 0 times 24974560 (70.13%) aligned exactly 1 time 9150319 (25.69%) aligned >1 times 95.82% overall alignment rate Time searching: 00:10:07 Overall time: 00:10:07 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] 4469222 / 34124879 = 0.1310 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 02:40:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981649/SRX3981649.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981649/SRX3981649.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981649/SRX3981649.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981649/SRX3981649.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 02:40:50: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:40:50: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:40:56: 1000000 INFO @ Tue, 30 Jun 2020 02:41:01: 2000000 INFO @ Tue, 30 Jun 2020 02:41:06: 3000000 INFO @ Tue, 30 Jun 2020 02:41:12: 4000000 INFO @ Tue, 30 Jun 2020 02:41:17: 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 02:41:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981649/SRX3981649.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981649/SRX3981649.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981649/SRX3981649.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981649/SRX3981649.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 02:41:20: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:41:20: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:41:22: 6000000 INFO @ Tue, 30 Jun 2020 02:41:26: 1000000 INFO @ Tue, 30 Jun 2020 02:41:28: 7000000 INFO @ Tue, 30 Jun 2020 02:41:32: 2000000 INFO @ Tue, 30 Jun 2020 02:41:33: 8000000 INFO @ Tue, 30 Jun 2020 02:41:39: 3000000 INFO @ Tue, 30 Jun 2020 02:41:39: 9000000 INFO @ Tue, 30 Jun 2020 02:41:44: 10000000 INFO @ Tue, 30 Jun 2020 02:41:45: 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 02:41:49: 11000000 INFO @ Tue, 30 Jun 2020 02:41:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3981649/SRX3981649.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3981649/SRX3981649.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3981649/SRX3981649.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3981649/SRX3981649.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 02:41:50: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:41:50: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:41:51: 5000000 INFO @ Tue, 30 Jun 2020 02:41:55: 12000000 INFO @ Tue, 30 Jun 2020 02:41:56: 1000000 INFO @ Tue, 30 Jun 2020 02:41:56: 6000000 INFO @ Tue, 30 Jun 2020 02:42:01: 13000000 INFO @ Tue, 30 Jun 2020 02:42:02: 2000000 INFO @ Tue, 30 Jun 2020 02:42:02: 7000000 INFO @ Tue, 30 Jun 2020 02:42:07: 14000000 INFO @ Tue, 30 Jun 2020 02:42:08: 3000000 INFO @ Tue, 30 Jun 2020 02:42:09: 8000000 INFO @ Tue, 30 Jun 2020 02:42:14: 15000000 INFO @ Tue, 30 Jun 2020 02:42:15: 4000000 INFO @ Tue, 30 Jun 2020 02:42:17: 9000000 INFO @ Tue, 30 Jun 2020 02:42:20: 16000000 INFO @ Tue, 30 Jun 2020 02:42:21: 5000000 INFO @ Tue, 30 Jun 2020 02:42:23: 10000000 INFO @ Tue, 30 Jun 2020 02:42:25: 17000000 INFO @ Tue, 30 Jun 2020 02:42:27: 6000000 INFO @ Tue, 30 Jun 2020 02:42:29: 11000000 INFO @ Tue, 30 Jun 2020 02:42:32: 18000000 INFO @ Tue, 30 Jun 2020 02:42:33: 7000000 INFO @ Tue, 30 Jun 2020 02:42:37: 12000000 INFO @ Tue, 30 Jun 2020 02:42:38: 19000000 INFO @ Tue, 30 Jun 2020 02:42:39: 8000000 INFO @ Tue, 30 Jun 2020 02:42:44: 20000000 INFO @ Tue, 30 Jun 2020 02:42:45: 13000000 INFO @ Tue, 30 Jun 2020 02:42:46: 9000000 INFO @ Tue, 30 Jun 2020 02:42:50: 21000000 INFO @ Tue, 30 Jun 2020 02:42:51: 14000000 INFO @ Tue, 30 Jun 2020 02:42:52: 10000000 INFO @ Tue, 30 Jun 2020 02:42:56: 22000000 INFO @ Tue, 30 Jun 2020 02:42:57: 15000000 INFO @ Tue, 30 Jun 2020 02:42:58: 11000000 INFO @ Tue, 30 Jun 2020 02:43:02: 23000000 INFO @ Tue, 30 Jun 2020 02:43:04: 12000000 INFO @ Tue, 30 Jun 2020 02:43:04: 16000000 INFO @ Tue, 30 Jun 2020 02:43:08: 24000000 INFO @ Tue, 30 Jun 2020 02:43:10: 13000000 INFO @ Tue, 30 Jun 2020 02:43:12: 17000000 INFO @ Tue, 30 Jun 2020 02:43:14: 25000000 INFO @ Tue, 30 Jun 2020 02:43:17: 14000000 INFO @ Tue, 30 Jun 2020 02:43:20: 18000000 INFO @ Tue, 30 Jun 2020 02:43:21: 26000000 INFO @ Tue, 30 Jun 2020 02:43:23: 15000000 INFO @ Tue, 30 Jun 2020 02:43:25: 19000000 INFO @ Tue, 30 Jun 2020 02:43:27: 27000000 INFO @ Tue, 30 Jun 2020 02:43:29: 16000000 INFO @ Tue, 30 Jun 2020 02:43:31: 20000000 INFO @ Tue, 30 Jun 2020 02:43:33: 28000000 INFO @ Tue, 30 Jun 2020 02:43:34: 17000000 INFO @ Tue, 30 Jun 2020 02:43:37: 21000000 INFO @ Tue, 30 Jun 2020 02:43:39: 29000000 INFO @ Tue, 30 Jun 2020 02:43:41: 18000000 INFO @ Tue, 30 Jun 2020 02:43:43: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:43:43: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:43:43: #1 total tags in treatment: 29655657 INFO @ Tue, 30 Jun 2020 02:43:43: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:43:43: #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 02:43:44: 22000000 INFO @ Tue, 30 Jun 2020 02:43:44: #1 tags after filtering in treatment: 29655607 INFO @ Tue, 30 Jun 2020 02:43:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:43:44: #1 finished! INFO @ Tue, 30 Jun 2020 02:43:44: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:43:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:43:46: 19000000 INFO @ Tue, 30 Jun 2020 02:43:46: #2 number of paired peaks: 261 WARNING @ Tue, 30 Jun 2020 02:43:46: Fewer paired peaks (261) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 261 pairs to build model! INFO @ Tue, 30 Jun 2020 02:43:46: start model_add_line... INFO @ Tue, 30 Jun 2020 02:43:46: start X-correlation... INFO @ Tue, 30 Jun 2020 02:43:47: end of X-cor INFO @ Tue, 30 Jun 2020 02:43:47: #2 finished! INFO @ Tue, 30 Jun 2020 02:43:47: #2 predicted fragment length is 49 bps INFO @ Tue, 30 Jun 2020 02:43:47: #2 alternative fragment length(s) may be 1,49,578 bps INFO @ Tue, 30 Jun 2020 02:43:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981649/SRX3981649.05_model.r WARNING @ Tue, 30 Jun 2020 02:43:47: #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 02:43:47: #2 You may need to consider one of the other alternative d(s): 1,49,578 WARNING @ Tue, 30 Jun 2020 02:43:47: #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 02:43:47: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:43:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:43:50: 23000000 INFO @ Tue, 30 Jun 2020 02:43:51: 20000000 INFO @ Tue, 30 Jun 2020 02:43:55: 24000000 INFO @ Tue, 30 Jun 2020 02:43:57: 21000000 INFO @ Tue, 30 Jun 2020 02:44:01: 25000000 INFO @ Tue, 30 Jun 2020 02:44:02: 22000000 INFO @ Tue, 30 Jun 2020 02:44:07: 23000000 INFO @ Tue, 30 Jun 2020 02:44:07: 26000000 INFO @ Tue, 30 Jun 2020 02:44:12: 24000000 INFO @ Tue, 30 Jun 2020 02:44:13: 27000000 INFO @ Tue, 30 Jun 2020 02:44:19: 25000000 INFO @ Tue, 30 Jun 2020 02:44:19: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:44:25: 29000000 INFO @ Tue, 30 Jun 2020 02:44:25: 26000000 INFO @ Tue, 30 Jun 2020 02:44:29: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:44:29: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:44:29: #1 total tags in treatment: 29655657 INFO @ Tue, 30 Jun 2020 02:44:29: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:44:29: #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 02:44:30: #1 tags after filtering in treatment: 29655607 INFO @ Tue, 30 Jun 2020 02:44:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:44:30: #1 finished! INFO @ Tue, 30 Jun 2020 02:44:30: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:44:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:44:31: 27000000 INFO @ Tue, 30 Jun 2020 02:44:32: #2 number of paired peaks: 261 WARNING @ Tue, 30 Jun 2020 02:44:32: Fewer paired peaks (261) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 261 pairs to build model! INFO @ Tue, 30 Jun 2020 02:44:32: start model_add_line... INFO @ Tue, 30 Jun 2020 02:44:32: start X-correlation... INFO @ Tue, 30 Jun 2020 02:44:32: end of X-cor INFO @ Tue, 30 Jun 2020 02:44:32: #2 finished! INFO @ Tue, 30 Jun 2020 02:44:32: #2 predicted fragment length is 49 bps INFO @ Tue, 30 Jun 2020 02:44:32: #2 alternative fragment length(s) may be 1,49,578 bps INFO @ Tue, 30 Jun 2020 02:44:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981649/SRX3981649.10_model.r WARNING @ Tue, 30 Jun 2020 02:44:32: #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 02:44:32: #2 You may need to consider one of the other alternative d(s): 1,49,578 WARNING @ Tue, 30 Jun 2020 02:44:32: #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 02:44:32: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:44:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:44:34: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:44:38: 28000000 INFO @ Tue, 30 Jun 2020 02:44:44: 29000000 INFO @ Tue, 30 Jun 2020 02:44:49: #1 tag size is determined as 51 bps INFO @ Tue, 30 Jun 2020 02:44:49: #1 tag size = 51 INFO @ Tue, 30 Jun 2020 02:44:49: #1 total tags in treatment: 29655657 INFO @ Tue, 30 Jun 2020 02:44:49: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:44:49: #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 02:44:50: #1 tags after filtering in treatment: 29655607 INFO @ Tue, 30 Jun 2020 02:44:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:44:50: #1 finished! INFO @ Tue, 30 Jun 2020 02:44:50: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:44:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:44:52: #2 number of paired peaks: 261 WARNING @ Tue, 30 Jun 2020 02:44:52: Fewer paired peaks (261) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 261 pairs to build model! INFO @ Tue, 30 Jun 2020 02:44:52: start model_add_line... INFO @ Tue, 30 Jun 2020 02:44:52: start X-correlation... INFO @ Tue, 30 Jun 2020 02:44:52: end of X-cor INFO @ Tue, 30 Jun 2020 02:44:52: #2 finished! INFO @ Tue, 30 Jun 2020 02:44:52: #2 predicted fragment length is 49 bps INFO @ Tue, 30 Jun 2020 02:44:52: #2 alternative fragment length(s) may be 1,49,578 bps INFO @ Tue, 30 Jun 2020 02:44:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3981649/SRX3981649.20_model.r WARNING @ Tue, 30 Jun 2020 02:44:52: #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 02:44:52: #2 You may need to consider one of the other alternative d(s): 1,49,578 WARNING @ Tue, 30 Jun 2020 02:44:52: #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 02:44:52: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:44:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:45:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981649/SRX3981649.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:45:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981649/SRX3981649.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:45:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981649/SRX3981649.05_summits.bed INFO @ Tue, 30 Jun 2020 02:45:00: Done! pass1 - making usageList (624 chroms): 2 millis pass2 - checking and writing primary data (3017 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:45:20: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:45:40: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:45:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981649/SRX3981649.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:45:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981649/SRX3981649.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:45:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981649/SRX3981649.10_summits.bed INFO @ Tue, 30 Jun 2020 02:45:44: Done! pass1 - making usageList (508 chroms): 1 millis pass2 - checking and writing primary data (2027 records, 4 fields): 31 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:46:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3981649/SRX3981649.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:46:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3981649/SRX3981649.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:46:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3981649/SRX3981649.20_summits.bed INFO @ Tue, 30 Jun 2020 02:46:06: Done! pass1 - making usageList (282 chroms): 1 millis pass2 - checking and writing primary data (680 records, 4 fields): 17 millis CompletedMACS2peakCalling