Job ID = 6458712 SRX = SRX5416213 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:35:22 prefetch.2.10.7: 1) Downloading 'SRR8617263'... 2020-06-21T12:35:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:45:01 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:45:02 prefetch.2.10.7: 1) 'SRR8617263' was downloaded successfully Read 49722557 spots for SRR8617263/SRR8617263.sra Written 49722557 spots for SRR8617263/SRR8617263.sra 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: 00:00:01 Multiseed full-index search: 00:13:03 49722557 reads; of these: 49722557 (100.00%) were unpaired; of these: 3283644 (6.60%) aligned 0 times 35113550 (70.62%) aligned exactly 1 time 11325363 (22.78%) aligned >1 times 93.40% overall alignment rate Time searching: 00:13:04 Overall time: 00:13:04 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 20 files... [bam_rmdupse_core] 14398408 / 46438913 = 0.3101 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 @ Sun, 21 Jun 2020 22:10:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5416213/SRX5416213.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5416213/SRX5416213.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5416213/SRX5416213.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5416213/SRX5416213.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 @ Sun, 21 Jun 2020 22:10:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:10:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:11:04: 1000000 INFO @ Sun, 21 Jun 2020 22:11:09: 2000000 INFO @ Sun, 21 Jun 2020 22:11:15: 3000000 INFO @ Sun, 21 Jun 2020 22:11:21: 4000000 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 @ Sun, 21 Jun 2020 22:11:26: 5000000 INFO @ Sun, 21 Jun 2020 22:11:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5416213/SRX5416213.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5416213/SRX5416213.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5416213/SRX5416213.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5416213/SRX5416213.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 @ Sun, 21 Jun 2020 22:11:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:11:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:11:33: 6000000 INFO @ Sun, 21 Jun 2020 22:11:35: 1000000 INFO @ Sun, 21 Jun 2020 22:11:41: 7000000 INFO @ Sun, 21 Jun 2020 22:11:43: 2000000 INFO @ Sun, 21 Jun 2020 22:11:48: 8000000 INFO @ Sun, 21 Jun 2020 22:11:51: 3000000 INFO @ Sun, 21 Jun 2020 22:11:55: 9000000 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 @ Sun, 21 Jun 2020 22:11:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5416213/SRX5416213.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5416213/SRX5416213.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5416213/SRX5416213.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5416213/SRX5416213.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 @ Sun, 21 Jun 2020 22:11:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:11:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:11:59: 4000000 INFO @ Sun, 21 Jun 2020 22:12:03: 10000000 INFO @ Sun, 21 Jun 2020 22:12:05: 1000000 INFO @ Sun, 21 Jun 2020 22:12:07: 5000000 INFO @ Sun, 21 Jun 2020 22:12:10: 11000000 INFO @ Sun, 21 Jun 2020 22:12:13: 2000000 INFO @ Sun, 21 Jun 2020 22:12:15: 6000000 INFO @ Sun, 21 Jun 2020 22:12:17: 12000000 INFO @ Sun, 21 Jun 2020 22:12:21: 3000000 INFO @ Sun, 21 Jun 2020 22:12:23: 7000000 INFO @ Sun, 21 Jun 2020 22:12:24: 13000000 INFO @ Sun, 21 Jun 2020 22:12:29: 4000000 INFO @ Sun, 21 Jun 2020 22:12:30: 8000000 INFO @ Sun, 21 Jun 2020 22:12:32: 14000000 INFO @ Sun, 21 Jun 2020 22:12:37: 5000000 INFO @ Sun, 21 Jun 2020 22:12:38: 9000000 INFO @ Sun, 21 Jun 2020 22:12:39: 15000000 INFO @ Sun, 21 Jun 2020 22:12:45: 6000000 INFO @ Sun, 21 Jun 2020 22:12:46: 16000000 INFO @ Sun, 21 Jun 2020 22:12:46: 10000000 INFO @ Sun, 21 Jun 2020 22:12:53: 7000000 INFO @ Sun, 21 Jun 2020 22:12:53: 17000000 INFO @ Sun, 21 Jun 2020 22:12:54: 11000000 INFO @ Sun, 21 Jun 2020 22:13:01: 18000000 INFO @ Sun, 21 Jun 2020 22:13:01: 8000000 INFO @ Sun, 21 Jun 2020 22:13:02: 12000000 INFO @ Sun, 21 Jun 2020 22:13:08: 19000000 INFO @ Sun, 21 Jun 2020 22:13:09: 9000000 INFO @ Sun, 21 Jun 2020 22:13:10: 13000000 INFO @ Sun, 21 Jun 2020 22:13:15: 20000000 INFO @ Sun, 21 Jun 2020 22:13:16: 10000000 INFO @ Sun, 21 Jun 2020 22:13:17: 14000000 INFO @ Sun, 21 Jun 2020 22:13:23: 21000000 INFO @ Sun, 21 Jun 2020 22:13:24: 11000000 INFO @ Sun, 21 Jun 2020 22:13:25: 15000000 INFO @ Sun, 21 Jun 2020 22:13:30: 22000000 INFO @ Sun, 21 Jun 2020 22:13:32: 12000000 INFO @ Sun, 21 Jun 2020 22:13:33: 16000000 INFO @ Sun, 21 Jun 2020 22:13:37: 23000000 INFO @ Sun, 21 Jun 2020 22:13:40: 13000000 INFO @ Sun, 21 Jun 2020 22:13:41: 17000000 INFO @ Sun, 21 Jun 2020 22:13:45: 24000000 INFO @ Sun, 21 Jun 2020 22:13:47: 14000000 INFO @ Sun, 21 Jun 2020 22:13:49: 18000000 INFO @ Sun, 21 Jun 2020 22:13:52: 25000000 INFO @ Sun, 21 Jun 2020 22:13:55: 15000000 INFO @ Sun, 21 Jun 2020 22:13:57: 19000000 INFO @ Sun, 21 Jun 2020 22:13:59: 26000000 INFO @ Sun, 21 Jun 2020 22:14:03: 16000000 INFO @ Sun, 21 Jun 2020 22:14:04: 20000000 INFO @ Sun, 21 Jun 2020 22:14:06: 27000000 INFO @ Sun, 21 Jun 2020 22:14:11: 17000000 INFO @ Sun, 21 Jun 2020 22:14:12: 21000000 INFO @ Sun, 21 Jun 2020 22:14:14: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:14:19: 18000000 INFO @ Sun, 21 Jun 2020 22:14:20: 22000000 INFO @ Sun, 21 Jun 2020 22:14:21: 29000000 INFO @ Sun, 21 Jun 2020 22:14:27: 19000000 INFO @ Sun, 21 Jun 2020 22:14:28: 23000000 INFO @ Sun, 21 Jun 2020 22:14:28: 30000000 INFO @ Sun, 21 Jun 2020 22:14:34: 20000000 INFO @ Sun, 21 Jun 2020 22:14:35: 31000000 INFO @ Sun, 21 Jun 2020 22:14:35: 24000000 INFO @ Sun, 21 Jun 2020 22:14:42: 21000000 INFO @ Sun, 21 Jun 2020 22:14:43: 32000000 INFO @ Sun, 21 Jun 2020 22:14:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:14:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:14:43: #1 total tags in treatment: 32040505 INFO @ Sun, 21 Jun 2020 22:14:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:14:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:14:43: 25000000 INFO @ Sun, 21 Jun 2020 22:14:44: #1 tags after filtering in treatment: 32040505 INFO @ Sun, 21 Jun 2020 22:14:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:14:44: #1 finished! INFO @ Sun, 21 Jun 2020 22:14:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:14:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:14:46: #2 number of paired peaks: 449 WARNING @ Sun, 21 Jun 2020 22:14:46: Fewer paired peaks (449) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 449 pairs to build model! INFO @ Sun, 21 Jun 2020 22:14:46: start model_add_line... INFO @ Sun, 21 Jun 2020 22:14:46: start X-correlation... INFO @ Sun, 21 Jun 2020 22:14:46: end of X-cor INFO @ Sun, 21 Jun 2020 22:14:46: #2 finished! INFO @ Sun, 21 Jun 2020 22:14:46: #2 predicted fragment length is 79 bps INFO @ Sun, 21 Jun 2020 22:14:46: #2 alternative fragment length(s) may be 3,79 bps INFO @ Sun, 21 Jun 2020 22:14:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5416213/SRX5416213.05_model.r WARNING @ Sun, 21 Jun 2020 22:14:46: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:14:46: #2 You may need to consider one of the other alternative d(s): 3,79 WARNING @ Sun, 21 Jun 2020 22:14:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:14:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:14:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:14:49: 22000000 INFO @ Sun, 21 Jun 2020 22:14:51: 26000000 INFO @ Sun, 21 Jun 2020 22:14:57: 23000000 INFO @ Sun, 21 Jun 2020 22:14:58: 27000000 INFO @ Sun, 21 Jun 2020 22:15:04: 24000000 INFO @ Sun, 21 Jun 2020 22:15:05: 28000000 INFO @ Sun, 21 Jun 2020 22:15:11: 25000000 INFO @ Sun, 21 Jun 2020 22:15:12: 29000000 INFO @ Sun, 21 Jun 2020 22:15:18: 26000000 INFO @ Sun, 21 Jun 2020 22:15:19: 30000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:15:25: 27000000 INFO @ Sun, 21 Jun 2020 22:15:26: 31000000 INFO @ Sun, 21 Jun 2020 22:15:32: 28000000 INFO @ Sun, 21 Jun 2020 22:15:33: 32000000 INFO @ Sun, 21 Jun 2020 22:15:34: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:15:34: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:15:34: #1 total tags in treatment: 32040505 INFO @ Sun, 21 Jun 2020 22:15:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:15:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:15:35: #1 tags after filtering in treatment: 32040505 INFO @ Sun, 21 Jun 2020 22:15:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:15:35: #1 finished! INFO @ Sun, 21 Jun 2020 22:15:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:15:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:15:37: #2 number of paired peaks: 449 WARNING @ Sun, 21 Jun 2020 22:15:37: Fewer paired peaks (449) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 449 pairs to build model! INFO @ Sun, 21 Jun 2020 22:15:37: start model_add_line... INFO @ Sun, 21 Jun 2020 22:15:37: start X-correlation... INFO @ Sun, 21 Jun 2020 22:15:37: end of X-cor INFO @ Sun, 21 Jun 2020 22:15:37: #2 finished! INFO @ Sun, 21 Jun 2020 22:15:37: #2 predicted fragment length is 79 bps INFO @ Sun, 21 Jun 2020 22:15:37: #2 alternative fragment length(s) may be 3,79 bps INFO @ Sun, 21 Jun 2020 22:15:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5416213/SRX5416213.10_model.r WARNING @ Sun, 21 Jun 2020 22:15:37: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:15:37: #2 You may need to consider one of the other alternative d(s): 3,79 WARNING @ Sun, 21 Jun 2020 22:15:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:15:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:15:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:15:39: 29000000 INFO @ Sun, 21 Jun 2020 22:15:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:15:46: 30000000 INFO @ Sun, 21 Jun 2020 22:15:52: 31000000 INFO @ Sun, 21 Jun 2020 22:15:59: 32000000 INFO @ Sun, 21 Jun 2020 22:16:00: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:16:00: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:16:00: #1 total tags in treatment: 32040505 INFO @ Sun, 21 Jun 2020 22:16:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:16:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:16:01: #1 tags after filtering in treatment: 32040505 INFO @ Sun, 21 Jun 2020 22:16:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:16:01: #1 finished! INFO @ Sun, 21 Jun 2020 22:16:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:16:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:16:03: #2 number of paired peaks: 449 WARNING @ Sun, 21 Jun 2020 22:16:03: Fewer paired peaks (449) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 449 pairs to build model! INFO @ Sun, 21 Jun 2020 22:16:03: start model_add_line... INFO @ Sun, 21 Jun 2020 22:16:03: start X-correlation... INFO @ Sun, 21 Jun 2020 22:16:03: end of X-cor INFO @ Sun, 21 Jun 2020 22:16:03: #2 finished! INFO @ Sun, 21 Jun 2020 22:16:03: #2 predicted fragment length is 79 bps INFO @ Sun, 21 Jun 2020 22:16:03: #2 alternative fragment length(s) may be 3,79 bps INFO @ Sun, 21 Jun 2020 22:16:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5416213/SRX5416213.20_model.r WARNING @ Sun, 21 Jun 2020 22:16:03: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:16:03: #2 You may need to consider one of the other alternative d(s): 3,79 WARNING @ Sun, 21 Jun 2020 22:16:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:16:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:16:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:16:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5416213/SRX5416213.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:16:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5416213/SRX5416213.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:16:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5416213/SRX5416213.05_summits.bed INFO @ Sun, 21 Jun 2020 22:16:07: Done! pass1 - making usageList (671 chroms): 2 millis pass2 - checking and writing primary data (5998 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:16:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:16:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5416213/SRX5416213.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:16:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5416213/SRX5416213.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:16:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5416213/SRX5416213.10_summits.bed INFO @ Sun, 21 Jun 2020 22:16:55: Done! pass1 - making usageList (578 chroms): 1 millis pass2 - checking and writing primary data (3425 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:16:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:17:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5416213/SRX5416213.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:17:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5416213/SRX5416213.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:17:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5416213/SRX5416213.20_summits.bed INFO @ Sun, 21 Jun 2020 22:17:22: Done! pass1 - making usageList (443 chroms): 3 millis pass2 - checking and writing primary data (1963 records, 4 fields): 15 millis CompletedMACS2peakCalling