Job ID = 6458152 SRX = SRX495268 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:32:04 prefetch.2.10.7: 1) Downloading 'SRR1198773'... 2020-06-21T12:32:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:36:23 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:36:23 prefetch.2.10.7: 1) 'SRR1198773' was downloaded successfully Read 25162813 spots for SRR1198773/SRR1198773.sra Written 25162813 spots for SRR1198773/SRR1198773.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: 00:00:00 Multiseed full-index search: 00:06:53 25162813 reads; of these: 25162813 (100.00%) were unpaired; of these: 1448186 (5.76%) aligned 0 times 16797599 (66.76%) aligned exactly 1 time 6917028 (27.49%) aligned >1 times 94.24% overall alignment rate Time searching: 00:06:53 Overall time: 00:06:53 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] 6320107 / 23714627 = 0.2665 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 21:49:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495268/SRX495268.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495268/SRX495268.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495268/SRX495268.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495268/SRX495268.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 21:49:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:49:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:49:54: 1000000 INFO @ Sun, 21 Jun 2020 21:49:59: 2000000 INFO @ Sun, 21 Jun 2020 21:50:04: 3000000 INFO @ Sun, 21 Jun 2020 21:50:10: 4000000 INFO @ Sun, 21 Jun 2020 21:50:15: 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 @ Sun, 21 Jun 2020 21:50:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495268/SRX495268.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495268/SRX495268.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495268/SRX495268.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495268/SRX495268.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 21:50:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:50:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:50:20: 6000000 INFO @ Sun, 21 Jun 2020 21:50:25: 1000000 INFO @ Sun, 21 Jun 2020 21:50:25: 7000000 INFO @ Sun, 21 Jun 2020 21:50:30: 2000000 INFO @ Sun, 21 Jun 2020 21:50:30: 8000000 INFO @ Sun, 21 Jun 2020 21:50:35: 3000000 INFO @ Sun, 21 Jun 2020 21:50:36: 9000000 INFO @ Sun, 21 Jun 2020 21:50:40: 4000000 INFO @ Sun, 21 Jun 2020 21:50:41: 10000000 INFO @ Sun, 21 Jun 2020 21:50:46: 5000000 INFO @ Sun, 21 Jun 2020 21:50:47: 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 @ Sun, 21 Jun 2020 21:50:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495268/SRX495268.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495268/SRX495268.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495268/SRX495268.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495268/SRX495268.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 21:50:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:50:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:50:51: 6000000 INFO @ Sun, 21 Jun 2020 21:50:52: 12000000 INFO @ Sun, 21 Jun 2020 21:50:55: 1000000 INFO @ Sun, 21 Jun 2020 21:50:56: 7000000 INFO @ Sun, 21 Jun 2020 21:50:58: 13000000 INFO @ Sun, 21 Jun 2020 21:51:00: 2000000 INFO @ Sun, 21 Jun 2020 21:51:02: 8000000 INFO @ Sun, 21 Jun 2020 21:51:03: 14000000 INFO @ Sun, 21 Jun 2020 21:51:06: 3000000 INFO @ Sun, 21 Jun 2020 21:51:07: 9000000 INFO @ Sun, 21 Jun 2020 21:51:09: 15000000 INFO @ Sun, 21 Jun 2020 21:51:11: 4000000 INFO @ Sun, 21 Jun 2020 21:51:12: 10000000 INFO @ Sun, 21 Jun 2020 21:51:14: 16000000 INFO @ Sun, 21 Jun 2020 21:51:16: 5000000 INFO @ Sun, 21 Jun 2020 21:51:18: 11000000 INFO @ Sun, 21 Jun 2020 21:51:19: 17000000 INFO @ Sun, 21 Jun 2020 21:51:22: 6000000 INFO @ Sun, 21 Jun 2020 21:51:22: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:51:22: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:51:22: #1 total tags in treatment: 17394520 INFO @ Sun, 21 Jun 2020 21:51:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:51:22: #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 21:51:22: #1 tags after filtering in treatment: 17394441 INFO @ Sun, 21 Jun 2020 21:51:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:51:22: #1 finished! INFO @ Sun, 21 Jun 2020 21:51:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:51:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:51:23: 12000000 INFO @ Sun, 21 Jun 2020 21:51:23: #2 number of paired peaks: 252 WARNING @ Sun, 21 Jun 2020 21:51:23: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Sun, 21 Jun 2020 21:51:23: start model_add_line... INFO @ Sun, 21 Jun 2020 21:51:24: start X-correlation... INFO @ Sun, 21 Jun 2020 21:51:24: end of X-cor INFO @ Sun, 21 Jun 2020 21:51:24: #2 finished! INFO @ Sun, 21 Jun 2020 21:51:24: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 21:51:24: #2 alternative fragment length(s) may be 2,47,178,336,441,467,490,532,540,561 bps INFO @ Sun, 21 Jun 2020 21:51:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495268/SRX495268.05_model.r WARNING @ Sun, 21 Jun 2020 21:51:24: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:51:24: #2 You may need to consider one of the other alternative d(s): 2,47,178,336,441,467,490,532,540,561 WARNING @ Sun, 21 Jun 2020 21:51:24: #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 21:51:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:51:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:51:27: 7000000 INFO @ Sun, 21 Jun 2020 21:51:28: 13000000 INFO @ Sun, 21 Jun 2020 21:51:32: 8000000 INFO @ Sun, 21 Jun 2020 21:51:33: 14000000 INFO @ Sun, 21 Jun 2020 21:51:37: 9000000 INFO @ Sun, 21 Jun 2020 21:51:39: 15000000 INFO @ Sun, 21 Jun 2020 21:51:43: 10000000 INFO @ Sun, 21 Jun 2020 21:51:44: 16000000 INFO @ Sun, 21 Jun 2020 21:51:48: 11000000 INFO @ Sun, 21 Jun 2020 21:51:49: 17000000 INFO @ Sun, 21 Jun 2020 21:51:51: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:51:51: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:51:51: #1 total tags in treatment: 17394520 INFO @ Sun, 21 Jun 2020 21:51:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:51:51: #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 21:51:52: #1 tags after filtering in treatment: 17394441 INFO @ Sun, 21 Jun 2020 21:51:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:51:52: #1 finished! INFO @ Sun, 21 Jun 2020 21:51:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:51:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:51:53: #2 number of paired peaks: 252 WARNING @ Sun, 21 Jun 2020 21:51:53: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Sun, 21 Jun 2020 21:51:53: start model_add_line... INFO @ Sun, 21 Jun 2020 21:51:53: start X-correlation... INFO @ Sun, 21 Jun 2020 21:51:53: end of X-cor INFO @ Sun, 21 Jun 2020 21:51:53: #2 finished! INFO @ Sun, 21 Jun 2020 21:51:53: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 21:51:53: #2 alternative fragment length(s) may be 2,47,178,336,441,467,490,532,540,561 bps INFO @ Sun, 21 Jun 2020 21:51:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495268/SRX495268.10_model.r WARNING @ Sun, 21 Jun 2020 21:51:53: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:51:53: #2 You may need to consider one of the other alternative d(s): 2,47,178,336,441,467,490,532,540,561 WARNING @ Sun, 21 Jun 2020 21:51:53: #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 21:51:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:51:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:51:53: 12000000 INFO @ Sun, 21 Jun 2020 21:51:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:51:58: 13000000 INFO @ Sun, 21 Jun 2020 21:52:03: 14000000 INFO @ Sun, 21 Jun 2020 21:52:08: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:52:13: 16000000 INFO @ Sun, 21 Jun 2020 21:52:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495268/SRX495268.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:52:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495268/SRX495268.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:52:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495268/SRX495268.05_summits.bed INFO @ Sun, 21 Jun 2020 21:52:15: Done! pass1 - making usageList (427 chroms): 2 millis pass2 - checking and writing primary data (1494 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:52:18: 17000000 INFO @ Sun, 21 Jun 2020 21:52:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:52:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:52:20: #1 total tags in treatment: 17394520 INFO @ Sun, 21 Jun 2020 21:52:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:52:20: #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 21:52:21: #1 tags after filtering in treatment: 17394441 INFO @ Sun, 21 Jun 2020 21:52:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:52:21: #1 finished! INFO @ Sun, 21 Jun 2020 21:52:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:52:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:52:22: #2 number of paired peaks: 252 WARNING @ Sun, 21 Jun 2020 21:52:22: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Sun, 21 Jun 2020 21:52:22: start model_add_line... INFO @ Sun, 21 Jun 2020 21:52:22: start X-correlation... INFO @ Sun, 21 Jun 2020 21:52:22: end of X-cor INFO @ Sun, 21 Jun 2020 21:52:22: #2 finished! INFO @ Sun, 21 Jun 2020 21:52:22: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 21:52:22: #2 alternative fragment length(s) may be 2,47,178,336,441,467,490,532,540,561 bps INFO @ Sun, 21 Jun 2020 21:52:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495268/SRX495268.20_model.r WARNING @ Sun, 21 Jun 2020 21:52:22: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:52:22: #2 You may need to consider one of the other alternative d(s): 2,47,178,336,441,467,490,532,540,561 WARNING @ Sun, 21 Jun 2020 21:52:22: #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 21:52:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:52:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:52:26: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:52:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495268/SRX495268.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:52:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495268/SRX495268.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:52:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495268/SRX495268.10_summits.bed INFO @ Sun, 21 Jun 2020 21:52:42: Done! pass1 - making usageList (177 chroms): 1 millis pass2 - checking and writing primary data (492 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:52:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:53:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495268/SRX495268.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:53:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495268/SRX495268.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:53:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495268/SRX495268.20_summits.bed INFO @ Sun, 21 Jun 2020 21:53:12: Done! pass1 - making usageList (86 chroms): 1 millis pass2 - checking and writing primary data (179 records, 4 fields): 4 millis CompletedMACS2peakCalling