Job ID = 6458839 SRX = SRX5661485 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:51:56 prefetch.2.10.7: 1) Downloading 'SRR8874492'... 2020-06-21T12:51:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:55:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:55:50 prefetch.2.10.7: 1) 'SRR8874492' was downloaded successfully 2020-06-21T12:55:50 prefetch.2.10.7: 'SRR8874492' has 0 unresolved dependencies Read 40141682 spots for SRR8874492/SRR8874492.sra Written 40141682 spots for SRR8874492/SRR8874492.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: 00:12:41 40141682 reads; of these: 40141682 (100.00%) were unpaired; of these: 4988122 (12.43%) aligned 0 times 25608708 (63.80%) aligned exactly 1 time 9544852 (23.78%) aligned >1 times 87.57% overall alignment rate Time searching: 00:12:41 Overall time: 00:12:41 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] 18675967 / 35153560 = 0.5313 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 22:17:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5661485/SRX5661485.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5661485/SRX5661485.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5661485/SRX5661485.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5661485/SRX5661485.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 22:17:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:17:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:17:13: 1000000 INFO @ Sun, 21 Jun 2020 22:17:20: 2000000 INFO @ Sun, 21 Jun 2020 22:17:28: 3000000 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 22:17:35: 4000000 INFO @ Sun, 21 Jun 2020 22:17:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5661485/SRX5661485.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5661485/SRX5661485.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5661485/SRX5661485.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5661485/SRX5661485.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 22:17:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:17:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:17:43: 5000000 INFO @ Sun, 21 Jun 2020 22:17:44: 1000000 INFO @ Sun, 21 Jun 2020 22:17:52: 6000000 INFO @ Sun, 21 Jun 2020 22:17:52: 2000000 INFO @ Sun, 21 Jun 2020 22:18:00: 3000000 INFO @ Sun, 21 Jun 2020 22:18:00: 7000000 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 22:18:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5661485/SRX5661485.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5661485/SRX5661485.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5661485/SRX5661485.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5661485/SRX5661485.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 22:18:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:18:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:18:09: 4000000 INFO @ Sun, 21 Jun 2020 22:18:09: 8000000 INFO @ Sun, 21 Jun 2020 22:18:13: 1000000 INFO @ Sun, 21 Jun 2020 22:18:17: 5000000 INFO @ Sun, 21 Jun 2020 22:18:18: 9000000 INFO @ Sun, 21 Jun 2020 22:18:22: 2000000 INFO @ Sun, 21 Jun 2020 22:18:26: 6000000 INFO @ Sun, 21 Jun 2020 22:18:27: 10000000 INFO @ Sun, 21 Jun 2020 22:18:30: 3000000 INFO @ Sun, 21 Jun 2020 22:18:35: 7000000 INFO @ Sun, 21 Jun 2020 22:18:35: 11000000 INFO @ Sun, 21 Jun 2020 22:18:39: 4000000 INFO @ Sun, 21 Jun 2020 22:18:43: 8000000 INFO @ Sun, 21 Jun 2020 22:18:44: 12000000 INFO @ Sun, 21 Jun 2020 22:18:47: 5000000 INFO @ Sun, 21 Jun 2020 22:18:52: 9000000 INFO @ Sun, 21 Jun 2020 22:18:52: 13000000 INFO @ Sun, 21 Jun 2020 22:18:56: 6000000 INFO @ Sun, 21 Jun 2020 22:19:00: 10000000 INFO @ Sun, 21 Jun 2020 22:19:01: 14000000 INFO @ Sun, 21 Jun 2020 22:19:04: 7000000 INFO @ Sun, 21 Jun 2020 22:19:09: 11000000 INFO @ Sun, 21 Jun 2020 22:19:10: 15000000 INFO @ Sun, 21 Jun 2020 22:19:13: 8000000 INFO @ Sun, 21 Jun 2020 22:19:17: 12000000 INFO @ Sun, 21 Jun 2020 22:19:19: 16000000 INFO @ Sun, 21 Jun 2020 22:19:21: 9000000 INFO @ Sun, 21 Jun 2020 22:19:23: #1 tag size is determined as 62 bps INFO @ Sun, 21 Jun 2020 22:19:23: #1 tag size = 62 INFO @ Sun, 21 Jun 2020 22:19:23: #1 total tags in treatment: 16477593 INFO @ Sun, 21 Jun 2020 22:19:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:19:23: #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 22:19:23: #1 tags after filtering in treatment: 16477590 INFO @ Sun, 21 Jun 2020 22:19:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:19:23: #1 finished! INFO @ Sun, 21 Jun 2020 22:19:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:19:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:19:24: #2 number of paired peaks: 602 WARNING @ Sun, 21 Jun 2020 22:19:24: Fewer paired peaks (602) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 602 pairs to build model! INFO @ Sun, 21 Jun 2020 22:19:24: start model_add_line... INFO @ Sun, 21 Jun 2020 22:19:24: start X-correlation... INFO @ Sun, 21 Jun 2020 22:19:24: end of X-cor INFO @ Sun, 21 Jun 2020 22:19:24: #2 finished! INFO @ Sun, 21 Jun 2020 22:19:24: #2 predicted fragment length is 63 bps INFO @ Sun, 21 Jun 2020 22:19:24: #2 alternative fragment length(s) may be 4,63,573 bps INFO @ Sun, 21 Jun 2020 22:19:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5661485/SRX5661485.05_model.r WARNING @ Sun, 21 Jun 2020 22:19:24: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:19:24: #2 You may need to consider one of the other alternative d(s): 4,63,573 WARNING @ Sun, 21 Jun 2020 22:19:24: #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 22:19:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:19:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:19:26: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:19:29: 10000000 INFO @ Sun, 21 Jun 2020 22:19:34: 14000000 INFO @ Sun, 21 Jun 2020 22:19:37: 11000000 INFO @ Sun, 21 Jun 2020 22:19:42: 15000000 INFO @ Sun, 21 Jun 2020 22:19:45: 12000000 INFO @ Sun, 21 Jun 2020 22:19:51: 16000000 INFO @ Sun, 21 Jun 2020 22:19:54: 13000000 INFO @ Sun, 21 Jun 2020 22:19:55: #1 tag size is determined as 62 bps INFO @ Sun, 21 Jun 2020 22:19:55: #1 tag size = 62 INFO @ Sun, 21 Jun 2020 22:19:55: #1 total tags in treatment: 16477593 INFO @ Sun, 21 Jun 2020 22:19:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:19:55: #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 22:19:55: #1 tags after filtering in treatment: 16477590 INFO @ Sun, 21 Jun 2020 22:19:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:19:55: #1 finished! INFO @ Sun, 21 Jun 2020 22:19:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:19:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:19:56: #2 number of paired peaks: 602 WARNING @ Sun, 21 Jun 2020 22:19:56: Fewer paired peaks (602) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 602 pairs to build model! INFO @ Sun, 21 Jun 2020 22:19:56: start model_add_line... INFO @ Sun, 21 Jun 2020 22:19:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:19:57: start X-correlation... INFO @ Sun, 21 Jun 2020 22:19:57: end of X-cor INFO @ Sun, 21 Jun 2020 22:19:57: #2 finished! INFO @ Sun, 21 Jun 2020 22:19:57: #2 predicted fragment length is 63 bps INFO @ Sun, 21 Jun 2020 22:19:57: #2 alternative fragment length(s) may be 4,63,573 bps INFO @ Sun, 21 Jun 2020 22:19:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5661485/SRX5661485.10_model.r WARNING @ Sun, 21 Jun 2020 22:19:57: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:19:57: #2 You may need to consider one of the other alternative d(s): 4,63,573 WARNING @ Sun, 21 Jun 2020 22:19:57: #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 22:19:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:19:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:20:01: 14000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:20:09: 15000000 INFO @ Sun, 21 Jun 2020 22:20:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5661485/SRX5661485.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:20:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5661485/SRX5661485.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:20:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5661485/SRX5661485.05_summits.bed INFO @ Sun, 21 Jun 2020 22:20:12: Done! pass1 - making usageList (872 chroms): 2 millis pass2 - checking and writing primary data (4156 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:20:16: 16000000 INFO @ Sun, 21 Jun 2020 22:20:20: #1 tag size is determined as 62 bps INFO @ Sun, 21 Jun 2020 22:20:20: #1 tag size = 62 INFO @ Sun, 21 Jun 2020 22:20:20: #1 total tags in treatment: 16477593 INFO @ Sun, 21 Jun 2020 22:20:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:20:20: #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 22:20:20: #1 tags after filtering in treatment: 16477590 INFO @ Sun, 21 Jun 2020 22:20:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:20:20: #1 finished! INFO @ Sun, 21 Jun 2020 22:20:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:20:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:20:21: #2 number of paired peaks: 602 WARNING @ Sun, 21 Jun 2020 22:20:21: Fewer paired peaks (602) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 602 pairs to build model! INFO @ Sun, 21 Jun 2020 22:20:21: start model_add_line... INFO @ Sun, 21 Jun 2020 22:20:21: start X-correlation... INFO @ Sun, 21 Jun 2020 22:20:21: end of X-cor INFO @ Sun, 21 Jun 2020 22:20:21: #2 finished! INFO @ Sun, 21 Jun 2020 22:20:21: #2 predicted fragment length is 63 bps INFO @ Sun, 21 Jun 2020 22:20:21: #2 alternative fragment length(s) may be 4,63,573 bps INFO @ Sun, 21 Jun 2020 22:20:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5661485/SRX5661485.20_model.r WARNING @ Sun, 21 Jun 2020 22:20:21: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:20:21: #2 You may need to consider one of the other alternative d(s): 4,63,573 WARNING @ Sun, 21 Jun 2020 22:20:21: #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 22:20:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:20:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:20:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:20:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5661485/SRX5661485.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:20:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5661485/SRX5661485.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:20:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5661485/SRX5661485.10_summits.bed INFO @ Sun, 21 Jun 2020 22:20:44: Done! pass1 - making usageList (674 chroms): 1 millis pass2 - checking and writing primary data (2462 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:20:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:21:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5661485/SRX5661485.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:21:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5661485/SRX5661485.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:21:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5661485/SRX5661485.20_summits.bed INFO @ Sun, 21 Jun 2020 22:21:09: Done! pass1 - making usageList (490 chroms): 1 millis pass2 - checking and writing primary data (1160 records, 4 fields): 15 millis CompletedMACS2peakCalling