Job ID = 6456226 SRX = SRX331382 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:39:23 prefetch.2.10.7: 1) Downloading 'SRR947619'... 2020-06-21T10:39:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:44:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:44:22 prefetch.2.10.7: 1) 'SRR947619' was downloaded successfully Read 21559305 spots for SRR947619/SRR947619.sra Written 21559305 spots for SRR947619/SRR947619.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: 00:05:40 21559305 reads; of these: 21559305 (100.00%) were unpaired; of these: 1516201 (7.03%) aligned 0 times 15525219 (72.01%) aligned exactly 1 time 4517885 (20.96%) aligned >1 times 92.97% overall alignment rate Time searching: 00:05:40 Overall time: 00:05:40 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] 2295470 / 20043104 = 0.1145 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 19:56:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331382/SRX331382.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331382/SRX331382.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331382/SRX331382.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331382/SRX331382.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 19:56:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:56:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:56:22: 1000000 INFO @ Sun, 21 Jun 2020 19:56:26: 2000000 INFO @ Sun, 21 Jun 2020 19:56:31: 3000000 INFO @ Sun, 21 Jun 2020 19:56:36: 4000000 INFO @ Sun, 21 Jun 2020 19:56:41: 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 19:56:45: 6000000 INFO @ Sun, 21 Jun 2020 19:56:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331382/SRX331382.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331382/SRX331382.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331382/SRX331382.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331382/SRX331382.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 19:56:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:56:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:56:50: 7000000 INFO @ Sun, 21 Jun 2020 19:56:52: 1000000 INFO @ Sun, 21 Jun 2020 19:56:55: 8000000 INFO @ Sun, 21 Jun 2020 19:56:58: 2000000 INFO @ Sun, 21 Jun 2020 19:57:00: 9000000 INFO @ Sun, 21 Jun 2020 19:57:03: 3000000 INFO @ Sun, 21 Jun 2020 19:57:05: 10000000 INFO @ Sun, 21 Jun 2020 19:57:08: 4000000 INFO @ Sun, 21 Jun 2020 19:57:10: 11000000 INFO @ Sun, 21 Jun 2020 19:57:14: 5000000 INFO @ Sun, 21 Jun 2020 19:57:15: 12000000 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 19:57:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331382/SRX331382.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331382/SRX331382.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331382/SRX331382.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331382/SRX331382.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 19:57:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:57:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:57:19: 6000000 INFO @ Sun, 21 Jun 2020 19:57:19: 13000000 INFO @ Sun, 21 Jun 2020 19:57:22: 1000000 INFO @ Sun, 21 Jun 2020 19:57:24: 14000000 INFO @ Sun, 21 Jun 2020 19:57:24: 7000000 INFO @ Sun, 21 Jun 2020 19:57:27: 2000000 INFO @ Sun, 21 Jun 2020 19:57:30: 15000000 INFO @ Sun, 21 Jun 2020 19:57:30: 8000000 INFO @ Sun, 21 Jun 2020 19:57:32: 3000000 INFO @ Sun, 21 Jun 2020 19:57:35: 16000000 INFO @ Sun, 21 Jun 2020 19:57:36: 9000000 INFO @ Sun, 21 Jun 2020 19:57:37: 4000000 INFO @ Sun, 21 Jun 2020 19:57:40: 17000000 INFO @ Sun, 21 Jun 2020 19:57:41: 10000000 INFO @ Sun, 21 Jun 2020 19:57:42: 5000000 INFO @ Sun, 21 Jun 2020 19:57:44: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:57:44: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:57:44: #1 total tags in treatment: 17747634 INFO @ Sun, 21 Jun 2020 19:57:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:57:44: #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 19:57:44: #1 tags after filtering in treatment: 17747634 INFO @ Sun, 21 Jun 2020 19:57:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:57:44: #1 finished! INFO @ Sun, 21 Jun 2020 19:57:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:57:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:57:45: #2 number of paired peaks: 250 WARNING @ Sun, 21 Jun 2020 19:57:45: Fewer paired peaks (250) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 250 pairs to build model! INFO @ Sun, 21 Jun 2020 19:57:45: start model_add_line... INFO @ Sun, 21 Jun 2020 19:57:46: start X-correlation... INFO @ Sun, 21 Jun 2020 19:57:46: end of X-cor INFO @ Sun, 21 Jun 2020 19:57:46: #2 finished! INFO @ Sun, 21 Jun 2020 19:57:46: #2 predicted fragment length is 35 bps INFO @ Sun, 21 Jun 2020 19:57:46: #2 alternative fragment length(s) may be 4,35 bps INFO @ Sun, 21 Jun 2020 19:57:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331382/SRX331382.05_model.r WARNING @ Sun, 21 Jun 2020 19:57:46: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:57:46: #2 You may need to consider one of the other alternative d(s): 4,35 WARNING @ Sun, 21 Jun 2020 19:57:46: #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 19:57:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:57:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:57:47: 11000000 INFO @ Sun, 21 Jun 2020 19:57:47: 6000000 INFO @ Sun, 21 Jun 2020 19:57:52: 7000000 INFO @ Sun, 21 Jun 2020 19:57:52: 12000000 INFO @ Sun, 21 Jun 2020 19:57:57: 8000000 INFO @ Sun, 21 Jun 2020 19:57:58: 13000000 INFO @ Sun, 21 Jun 2020 19:58:02: 9000000 INFO @ Sun, 21 Jun 2020 19:58:03: 14000000 INFO @ Sun, 21 Jun 2020 19:58:07: 10000000 INFO @ Sun, 21 Jun 2020 19:58:09: 15000000 INFO @ Sun, 21 Jun 2020 19:58:11: 11000000 INFO @ Sun, 21 Jun 2020 19:58:15: 16000000 INFO @ Sun, 21 Jun 2020 19:58:16: 12000000 INFO @ Sun, 21 Jun 2020 19:58:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:58:20: 17000000 INFO @ Sun, 21 Jun 2020 19:58:21: 13000000 INFO @ Sun, 21 Jun 2020 19:58:24: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:58:24: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:58:24: #1 total tags in treatment: 17747634 INFO @ Sun, 21 Jun 2020 19:58:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:58:24: #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 19:58:25: #1 tags after filtering in treatment: 17747634 INFO @ Sun, 21 Jun 2020 19:58:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:58:25: #1 finished! INFO @ Sun, 21 Jun 2020 19:58:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:58:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:58:26: 14000000 INFO @ Sun, 21 Jun 2020 19:58:26: #2 number of paired peaks: 250 WARNING @ Sun, 21 Jun 2020 19:58:26: Fewer paired peaks (250) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 250 pairs to build model! INFO @ Sun, 21 Jun 2020 19:58:26: start model_add_line... INFO @ Sun, 21 Jun 2020 19:58:26: start X-correlation... INFO @ Sun, 21 Jun 2020 19:58:26: end of X-cor INFO @ Sun, 21 Jun 2020 19:58:26: #2 finished! INFO @ Sun, 21 Jun 2020 19:58:26: #2 predicted fragment length is 35 bps INFO @ Sun, 21 Jun 2020 19:58:26: #2 alternative fragment length(s) may be 4,35 bps INFO @ Sun, 21 Jun 2020 19:58:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331382/SRX331382.10_model.r WARNING @ Sun, 21 Jun 2020 19:58:26: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:58:26: #2 You may need to consider one of the other alternative d(s): 4,35 WARNING @ Sun, 21 Jun 2020 19:58:26: #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 19:58:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:58:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:58:31: 15000000 INFO @ Sun, 21 Jun 2020 19:58:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331382/SRX331382.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:58:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331382/SRX331382.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:58:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331382/SRX331382.05_summits.bed INFO @ Sun, 21 Jun 2020 19:58:33: Done! pass1 - making usageList (509 chroms): 1 millis pass2 - checking and writing primary data (2265 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:58:35: 16000000 INFO @ Sun, 21 Jun 2020 19:58:40: 17000000 INFO @ Sun, 21 Jun 2020 19:58:44: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:58:44: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:58:44: #1 total tags in treatment: 17747634 INFO @ Sun, 21 Jun 2020 19:58:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:58:44: #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 19:58:45: #1 tags after filtering in treatment: 17747634 INFO @ Sun, 21 Jun 2020 19:58:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:58:45: #1 finished! INFO @ Sun, 21 Jun 2020 19:58:45: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:58:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:58:46: #2 number of paired peaks: 250 WARNING @ Sun, 21 Jun 2020 19:58:46: Fewer paired peaks (250) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 250 pairs to build model! INFO @ Sun, 21 Jun 2020 19:58:46: start model_add_line... INFO @ Sun, 21 Jun 2020 19:58:46: start X-correlation... INFO @ Sun, 21 Jun 2020 19:58:46: end of X-cor INFO @ Sun, 21 Jun 2020 19:58:46: #2 finished! INFO @ Sun, 21 Jun 2020 19:58:46: #2 predicted fragment length is 35 bps INFO @ Sun, 21 Jun 2020 19:58:46: #2 alternative fragment length(s) may be 4,35 bps INFO @ Sun, 21 Jun 2020 19:58:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331382/SRX331382.20_model.r WARNING @ Sun, 21 Jun 2020 19:58:46: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:58:46: #2 You may need to consider one of the other alternative d(s): 4,35 WARNING @ Sun, 21 Jun 2020 19:58:46: #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 19:58:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:58:46: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:58:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:59:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331382/SRX331382.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:59:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331382/SRX331382.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:59:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331382/SRX331382.10_summits.bed INFO @ Sun, 21 Jun 2020 19:59:15: Done! pass1 - making usageList (392 chroms): 2 millis pass2 - checking and writing primary data (1161 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:59:18: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:59:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331382/SRX331382.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:59:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331382/SRX331382.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:59:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331382/SRX331382.20_summits.bed INFO @ Sun, 21 Jun 2020 19:59:34: Done! pass1 - making usageList (192 chroms): 1 millis pass2 - checking and writing primary data (410 records, 4 fields): 7 millis CompletedMACS2peakCalling