Job ID = 6456412 SRX = SRX3404009 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:10:09 prefetch.2.10.7: 1) Downloading 'SRR6303486'... 2020-06-21T11:10:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:12:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:12:15 prefetch.2.10.7: 'SRR6303486' is valid 2020-06-21T11:12:15 prefetch.2.10.7: 1) 'SRR6303486' was downloaded successfully 2020-06-21T11:12:15 prefetch.2.10.7: 'SRR6303486' has 0 unresolved dependencies Read 19218421 spots for SRR6303486/SRR6303486.sra Written 19218421 spots for SRR6303486/SRR6303486.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: 00:05:18 19218421 reads; of these: 19218421 (100.00%) were unpaired; of these: 556126 (2.89%) aligned 0 times 13819466 (71.91%) aligned exactly 1 time 4842829 (25.20%) aligned >1 times 97.11% overall alignment rate Time searching: 00:05:18 Overall time: 00:05:18 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 8 files... [bam_rmdupse_core] 1921466 / 18662295 = 0.1030 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 20:22:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404009/SRX3404009.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404009/SRX3404009.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404009/SRX3404009.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404009/SRX3404009.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 20:22:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:22:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:22:52: 1000000 INFO @ Sun, 21 Jun 2020 20:22:58: 2000000 INFO @ Sun, 21 Jun 2020 20:23:03: 3000000 INFO @ Sun, 21 Jun 2020 20:23:09: 4000000 INFO @ Sun, 21 Jun 2020 20:23:14: 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 20:23:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404009/SRX3404009.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404009/SRX3404009.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404009/SRX3404009.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404009/SRX3404009.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 20:23:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:23:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:23:20: 6000000 INFO @ Sun, 21 Jun 2020 20:23:23: 1000000 INFO @ Sun, 21 Jun 2020 20:23:25: 7000000 INFO @ Sun, 21 Jun 2020 20:23:29: 2000000 INFO @ Sun, 21 Jun 2020 20:23:31: 8000000 INFO @ Sun, 21 Jun 2020 20:23:35: 3000000 INFO @ Sun, 21 Jun 2020 20:23:37: 9000000 INFO @ Sun, 21 Jun 2020 20:23:41: 4000000 INFO @ Sun, 21 Jun 2020 20:23:43: 10000000 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 20:23:46: 5000000 INFO @ Sun, 21 Jun 2020 20:23:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3404009/SRX3404009.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3404009/SRX3404009.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3404009/SRX3404009.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3404009/SRX3404009.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 20:23:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:23:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:23:49: 11000000 INFO @ Sun, 21 Jun 2020 20:23:52: 6000000 INFO @ Sun, 21 Jun 2020 20:23:54: 1000000 INFO @ Sun, 21 Jun 2020 20:23:55: 12000000 INFO @ Sun, 21 Jun 2020 20:23:59: 7000000 INFO @ Sun, 21 Jun 2020 20:24:01: 2000000 INFO @ Sun, 21 Jun 2020 20:24:01: 13000000 INFO @ Sun, 21 Jun 2020 20:24:05: 8000000 INFO @ Sun, 21 Jun 2020 20:24:07: 14000000 INFO @ Sun, 21 Jun 2020 20:24:08: 3000000 INFO @ Sun, 21 Jun 2020 20:24:11: 9000000 INFO @ Sun, 21 Jun 2020 20:24:14: 15000000 INFO @ Sun, 21 Jun 2020 20:24:15: 4000000 INFO @ Sun, 21 Jun 2020 20:24:17: 10000000 INFO @ Sun, 21 Jun 2020 20:24:20: 16000000 INFO @ Sun, 21 Jun 2020 20:24:22: 5000000 INFO @ Sun, 21 Jun 2020 20:24:23: 11000000 INFO @ Sun, 21 Jun 2020 20:24:25: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:24:25: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:24:25: #1 total tags in treatment: 16740829 INFO @ Sun, 21 Jun 2020 20:24:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:24:25: #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 20:24:25: #1 tags after filtering in treatment: 16740752 INFO @ Sun, 21 Jun 2020 20:24:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:24:25: #1 finished! INFO @ Sun, 21 Jun 2020 20:24:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:24:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:24:26: #2 number of paired peaks: 751 WARNING @ Sun, 21 Jun 2020 20:24:26: Fewer paired peaks (751) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 751 pairs to build model! INFO @ Sun, 21 Jun 2020 20:24:26: start model_add_line... INFO @ Sun, 21 Jun 2020 20:24:27: start X-correlation... INFO @ Sun, 21 Jun 2020 20:24:27: end of X-cor INFO @ Sun, 21 Jun 2020 20:24:27: #2 finished! INFO @ Sun, 21 Jun 2020 20:24:27: #2 predicted fragment length is 62 bps INFO @ Sun, 21 Jun 2020 20:24:27: #2 alternative fragment length(s) may be 3,62 bps INFO @ Sun, 21 Jun 2020 20:24:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404009/SRX3404009.05_model.r WARNING @ Sun, 21 Jun 2020 20:24:27: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:24:27: #2 You may need to consider one of the other alternative d(s): 3,62 WARNING @ Sun, 21 Jun 2020 20:24:27: #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 20:24:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:24:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:24:29: 6000000 INFO @ Sun, 21 Jun 2020 20:24:29: 12000000 INFO @ Sun, 21 Jun 2020 20:24:35: 13000000 INFO @ Sun, 21 Jun 2020 20:24:36: 7000000 INFO @ Sun, 21 Jun 2020 20:24:41: 14000000 INFO @ Sun, 21 Jun 2020 20:24:43: 8000000 INFO @ Sun, 21 Jun 2020 20:24:48: 15000000 INFO @ Sun, 21 Jun 2020 20:24:50: 9000000 INFO @ Sun, 21 Jun 2020 20:24:54: 16000000 INFO @ Sun, 21 Jun 2020 20:24:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:24:57: 10000000 INFO @ Sun, 21 Jun 2020 20:24:59: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:24:59: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:24:59: #1 total tags in treatment: 16740829 INFO @ Sun, 21 Jun 2020 20:24:59: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:24:59: #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 20:24:59: #1 tags after filtering in treatment: 16740752 INFO @ Sun, 21 Jun 2020 20:24:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:24:59: #1 finished! INFO @ Sun, 21 Jun 2020 20:24:59: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:24:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:25:00: #2 number of paired peaks: 751 WARNING @ Sun, 21 Jun 2020 20:25:00: Fewer paired peaks (751) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 751 pairs to build model! INFO @ Sun, 21 Jun 2020 20:25:00: start model_add_line... INFO @ Sun, 21 Jun 2020 20:25:00: start X-correlation... INFO @ Sun, 21 Jun 2020 20:25:00: end of X-cor INFO @ Sun, 21 Jun 2020 20:25:00: #2 finished! INFO @ Sun, 21 Jun 2020 20:25:00: #2 predicted fragment length is 62 bps INFO @ Sun, 21 Jun 2020 20:25:00: #2 alternative fragment length(s) may be 3,62 bps INFO @ Sun, 21 Jun 2020 20:25:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404009/SRX3404009.10_model.r WARNING @ Sun, 21 Jun 2020 20:25:00: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:25:00: #2 You may need to consider one of the other alternative d(s): 3,62 WARNING @ Sun, 21 Jun 2020 20:25:00: #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 20:25:00: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:25:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:25:04: 11000000 INFO @ Sun, 21 Jun 2020 20:25:10: 12000000 INFO @ Sun, 21 Jun 2020 20:25:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404009/SRX3404009.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:25:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404009/SRX3404009.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:25:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404009/SRX3404009.05_summits.bed INFO @ Sun, 21 Jun 2020 20:25:12: Done! pass1 - making usageList (622 chroms): 2 millis pass2 - checking and writing primary data (2704 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:25:17: 13000000 INFO @ Sun, 21 Jun 2020 20:25:23: 14000000 INFO @ Sun, 21 Jun 2020 20:25:30: 15000000 INFO @ Sun, 21 Jun 2020 20:25:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:25:36: 16000000 INFO @ Sun, 21 Jun 2020 20:25:41: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:25:41: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:25:41: #1 total tags in treatment: 16740829 INFO @ Sun, 21 Jun 2020 20:25:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:25:41: #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 20:25:42: #1 tags after filtering in treatment: 16740752 INFO @ Sun, 21 Jun 2020 20:25:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:25:42: #1 finished! INFO @ Sun, 21 Jun 2020 20:25:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:25:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:25:43: #2 number of paired peaks: 751 WARNING @ Sun, 21 Jun 2020 20:25:43: Fewer paired peaks (751) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 751 pairs to build model! INFO @ Sun, 21 Jun 2020 20:25:43: start model_add_line... INFO @ Sun, 21 Jun 2020 20:25:43: start X-correlation... INFO @ Sun, 21 Jun 2020 20:25:43: end of X-cor INFO @ Sun, 21 Jun 2020 20:25:43: #2 finished! INFO @ Sun, 21 Jun 2020 20:25:43: #2 predicted fragment length is 62 bps INFO @ Sun, 21 Jun 2020 20:25:43: #2 alternative fragment length(s) may be 3,62 bps INFO @ Sun, 21 Jun 2020 20:25:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3404009/SRX3404009.20_model.r WARNING @ Sun, 21 Jun 2020 20:25:43: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:25:43: #2 You may need to consider one of the other alternative d(s): 3,62 WARNING @ Sun, 21 Jun 2020 20:25:43: #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 20:25:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:25:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:25:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404009/SRX3404009.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:25:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404009/SRX3404009.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:25:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404009/SRX3404009.10_summits.bed INFO @ Sun, 21 Jun 2020 20:25:47: Done! pass1 - making usageList (379 chroms): 1 millis pass2 - checking and writing primary data (1104 records, 4 fields): 12 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:26:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:26:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3404009/SRX3404009.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:26:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3404009/SRX3404009.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:26:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3404009/SRX3404009.20_summits.bed INFO @ Sun, 21 Jun 2020 20:26:30: Done! pass1 - making usageList (177 chroms): 1 millis pass2 - checking and writing primary data (476 records, 4 fields): 7 millis CompletedMACS2peakCalling