Job ID = 6456020 SRX = SRX3159477 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:28:51 prefetch.2.10.7: 1) Downloading 'SRR6004207'... 2020-06-21T10:28:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:31:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:31:34 prefetch.2.10.7: 'SRR6004207' is valid 2020-06-21T10:31:34 prefetch.2.10.7: 1) 'SRR6004207' was downloaded successfully 2020-06-21T10:31:34 prefetch.2.10.7: 'SRR6004207' has 0 unresolved dependencies Read 27474247 spots for SRR6004207/SRR6004207.sra Written 27474247 spots for SRR6004207/SRR6004207.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: 00:07:46 27474247 reads; of these: 27474247 (100.00%) were unpaired; of these: 965015 (3.51%) aligned 0 times 18508075 (67.37%) aligned exactly 1 time 8001157 (29.12%) aligned >1 times 96.49% overall alignment rate Time searching: 00:07:46 Overall time: 00:07:46 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] 3920703 / 26509232 = 0.1479 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 19:47:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159477/SRX3159477.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159477/SRX3159477.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159477/SRX3159477.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159477/SRX3159477.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 19:47:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:47:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:47:26: 1000000 INFO @ Sun, 21 Jun 2020 19:47:31: 2000000 INFO @ Sun, 21 Jun 2020 19:47:35: 3000000 INFO @ Sun, 21 Jun 2020 19:47:40: 4000000 INFO @ Sun, 21 Jun 2020 19:47:45: 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 19:47:50: 6000000 INFO @ Sun, 21 Jun 2020 19:47:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159477/SRX3159477.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159477/SRX3159477.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159477/SRX3159477.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159477/SRX3159477.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 19:47:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:47:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:47:55: 7000000 INFO @ Sun, 21 Jun 2020 19:47:56: 1000000 INFO @ Sun, 21 Jun 2020 19:48:00: 8000000 INFO @ Sun, 21 Jun 2020 19:48:01: 2000000 INFO @ Sun, 21 Jun 2020 19:48:05: 9000000 INFO @ Sun, 21 Jun 2020 19:48:06: 3000000 INFO @ Sun, 21 Jun 2020 19:48:10: 10000000 INFO @ Sun, 21 Jun 2020 19:48:11: 4000000 INFO @ Sun, 21 Jun 2020 19:48:15: 11000000 INFO @ Sun, 21 Jun 2020 19:48:17: 5000000 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 19:48:20: 12000000 INFO @ Sun, 21 Jun 2020 19:48:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3159477/SRX3159477.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3159477/SRX3159477.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3159477/SRX3159477.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3159477/SRX3159477.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 19:48:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:48:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:48:22: 6000000 INFO @ Sun, 21 Jun 2020 19:48:26: 13000000 INFO @ Sun, 21 Jun 2020 19:48:27: 1000000 INFO @ Sun, 21 Jun 2020 19:48:28: 7000000 INFO @ Sun, 21 Jun 2020 19:48:32: 14000000 INFO @ Sun, 21 Jun 2020 19:48:33: 2000000 INFO @ Sun, 21 Jun 2020 19:48:34: 8000000 INFO @ Sun, 21 Jun 2020 19:48:39: 15000000 INFO @ Sun, 21 Jun 2020 19:48:40: 3000000 INFO @ Sun, 21 Jun 2020 19:48:41: 9000000 INFO @ Sun, 21 Jun 2020 19:48:45: 16000000 INFO @ Sun, 21 Jun 2020 19:48:46: 4000000 INFO @ Sun, 21 Jun 2020 19:48:47: 10000000 INFO @ Sun, 21 Jun 2020 19:48:52: 17000000 INFO @ Sun, 21 Jun 2020 19:48:53: 5000000 INFO @ Sun, 21 Jun 2020 19:48:54: 11000000 INFO @ Sun, 21 Jun 2020 19:48:58: 18000000 INFO @ Sun, 21 Jun 2020 19:48:59: 6000000 INFO @ Sun, 21 Jun 2020 19:49:00: 12000000 INFO @ Sun, 21 Jun 2020 19:49:06: 19000000 INFO @ Sun, 21 Jun 2020 19:49:06: 7000000 INFO @ Sun, 21 Jun 2020 19:49:07: 13000000 INFO @ Sun, 21 Jun 2020 19:49:12: 20000000 INFO @ Sun, 21 Jun 2020 19:49:12: 8000000 INFO @ Sun, 21 Jun 2020 19:49:13: 14000000 INFO @ Sun, 21 Jun 2020 19:49:19: 21000000 INFO @ Sun, 21 Jun 2020 19:49:19: 9000000 INFO @ Sun, 21 Jun 2020 19:49:20: 15000000 INFO @ Sun, 21 Jun 2020 19:49:25: 10000000 INFO @ Sun, 21 Jun 2020 19:49:25: 22000000 INFO @ Sun, 21 Jun 2020 19:49:26: 16000000 INFO @ Sun, 21 Jun 2020 19:49:29: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:49:29: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:49:29: #1 total tags in treatment: 22588529 INFO @ Sun, 21 Jun 2020 19:49:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:49:29: #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 19:49:30: #1 tags after filtering in treatment: 22588529 INFO @ Sun, 21 Jun 2020 19:49:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:49:30: #1 finished! INFO @ Sun, 21 Jun 2020 19:49:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:49:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:49:30: 11000000 INFO @ Sun, 21 Jun 2020 19:49:31: #2 number of paired peaks: 487 WARNING @ Sun, 21 Jun 2020 19:49:31: Fewer paired peaks (487) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 487 pairs to build model! INFO @ Sun, 21 Jun 2020 19:49:31: start model_add_line... INFO @ Sun, 21 Jun 2020 19:49:31: start X-correlation... INFO @ Sun, 21 Jun 2020 19:49:31: end of X-cor INFO @ Sun, 21 Jun 2020 19:49:31: #2 finished! INFO @ Sun, 21 Jun 2020 19:49:31: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 19:49:31: #2 alternative fragment length(s) may be 1,32 bps INFO @ Sun, 21 Jun 2020 19:49:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159477/SRX3159477.05_model.r WARNING @ Sun, 21 Jun 2020 19:49:31: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:49:31: #2 You may need to consider one of the other alternative d(s): 1,32 WARNING @ Sun, 21 Jun 2020 19:49:31: #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 19:49:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:49:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:49:32: 17000000 INFO @ Sun, 21 Jun 2020 19:49:36: 12000000 INFO @ Sun, 21 Jun 2020 19:49:38: 18000000 INFO @ Sun, 21 Jun 2020 19:49:41: 13000000 INFO @ Sun, 21 Jun 2020 19:49:44: 19000000 INFO @ Sun, 21 Jun 2020 19:49:47: 14000000 INFO @ Sun, 21 Jun 2020 19:49:50: 20000000 INFO @ Sun, 21 Jun 2020 19:49:52: 15000000 INFO @ Sun, 21 Jun 2020 19:49:55: 21000000 INFO @ Sun, 21 Jun 2020 19:49:57: 16000000 INFO @ Sun, 21 Jun 2020 19:50:01: 22000000 INFO @ Sun, 21 Jun 2020 19:50:02: 17000000 INFO @ Sun, 21 Jun 2020 19:50:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:50:05: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:50:05: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:50:05: #1 total tags in treatment: 22588529 INFO @ Sun, 21 Jun 2020 19:50:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:50:05: #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 19:50:06: #1 tags after filtering in treatment: 22588529 INFO @ Sun, 21 Jun 2020 19:50:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:50:06: #1 finished! INFO @ Sun, 21 Jun 2020 19:50:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:50:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:50:07: #2 number of paired peaks: 487 WARNING @ Sun, 21 Jun 2020 19:50:07: Fewer paired peaks (487) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 487 pairs to build model! INFO @ Sun, 21 Jun 2020 19:50:07: start model_add_line... INFO @ Sun, 21 Jun 2020 19:50:07: start X-correlation... INFO @ Sun, 21 Jun 2020 19:50:08: end of X-cor INFO @ Sun, 21 Jun 2020 19:50:08: #2 finished! INFO @ Sun, 21 Jun 2020 19:50:08: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 19:50:08: #2 alternative fragment length(s) may be 1,32 bps INFO @ Sun, 21 Jun 2020 19:50:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159477/SRX3159477.10_model.r WARNING @ Sun, 21 Jun 2020 19:50:08: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:50:08: #2 You may need to consider one of the other alternative d(s): 1,32 WARNING @ Sun, 21 Jun 2020 19:50:08: #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 19:50:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:50:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:50:08: 18000000 INFO @ Sun, 21 Jun 2020 19:50:13: 19000000 INFO @ Sun, 21 Jun 2020 19:50:18: 20000000 INFO @ Sun, 21 Jun 2020 19:50:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159477/SRX3159477.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:50:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159477/SRX3159477.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:50:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159477/SRX3159477.05_summits.bed INFO @ Sun, 21 Jun 2020 19:50:21: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:50:23: 21000000 INFO @ Sun, 21 Jun 2020 19:50:28: 22000000 INFO @ Sun, 21 Jun 2020 19:50:31: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:50:31: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:50:31: #1 total tags in treatment: 22588529 INFO @ Sun, 21 Jun 2020 19:50:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:50:31: #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 19:50:32: #1 tags after filtering in treatment: 22588529 INFO @ Sun, 21 Jun 2020 19:50:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:50:32: #1 finished! INFO @ Sun, 21 Jun 2020 19:50:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:50:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:50:34: #2 number of paired peaks: 487 WARNING @ Sun, 21 Jun 2020 19:50:34: Fewer paired peaks (487) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 487 pairs to build model! INFO @ Sun, 21 Jun 2020 19:50:34: start model_add_line... INFO @ Sun, 21 Jun 2020 19:50:34: start X-correlation... INFO @ Sun, 21 Jun 2020 19:50:34: end of X-cor INFO @ Sun, 21 Jun 2020 19:50:34: #2 finished! INFO @ Sun, 21 Jun 2020 19:50:34: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 19:50:34: #2 alternative fragment length(s) may be 1,32 bps INFO @ Sun, 21 Jun 2020 19:50:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3159477/SRX3159477.20_model.r WARNING @ Sun, 21 Jun 2020 19:50:34: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:50:34: #2 You may need to consider one of the other alternative d(s): 1,32 WARNING @ Sun, 21 Jun 2020 19:50:34: #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 19:50:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:50:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:50:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:50:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159477/SRX3159477.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:50:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159477/SRX3159477.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:50:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159477/SRX3159477.10_summits.bed INFO @ Sun, 21 Jun 2020 19:50:57: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:51:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:51:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3159477/SRX3159477.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:51:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3159477/SRX3159477.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:51:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3159477/SRX3159477.20_summits.bed INFO @ Sun, 21 Jun 2020 19:51:23: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。