Job ID = 6453753 SRX = SRX1433397 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:40:48 prefetch.2.10.7: 1) Downloading 'SRR2919813'... 2020-06-21T08:40:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:47:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:47:56 prefetch.2.10.7: 1) 'SRR2919813' was downloaded successfully Read 37027407 spots for SRR2919813/SRR2919813.sra Written 37027407 spots for SRR2919813/SRR2919813.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: 00:08:48 37027407 reads; of these: 37027407 (100.00%) were unpaired; of these: 2731930 (7.38%) aligned 0 times 25229058 (68.14%) aligned exactly 1 time 9066419 (24.49%) aligned >1 times 92.62% overall alignment rate Time searching: 00:08:48 Overall time: 00:08:48 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] 7706634 / 34295477 = 0.2247 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 18:05:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433397/SRX1433397.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433397/SRX1433397.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433397/SRX1433397.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433397/SRX1433397.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 18:05:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:05:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:05:43: 1000000 INFO @ Sun, 21 Jun 2020 18:05:49: 2000000 INFO @ Sun, 21 Jun 2020 18:05:54: 3000000 INFO @ Sun, 21 Jun 2020 18:06:00: 4000000 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 18:06:05: 5000000 INFO @ Sun, 21 Jun 2020 18:06:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433397/SRX1433397.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433397/SRX1433397.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433397/SRX1433397.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433397/SRX1433397.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 18:06:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:06:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:06:11: 6000000 INFO @ Sun, 21 Jun 2020 18:06:13: 1000000 INFO @ Sun, 21 Jun 2020 18:06:18: 7000000 INFO @ Sun, 21 Jun 2020 18:06:20: 2000000 INFO @ Sun, 21 Jun 2020 18:06:24: 8000000 INFO @ Sun, 21 Jun 2020 18:06:26: 3000000 INFO @ Sun, 21 Jun 2020 18:06:30: 9000000 INFO @ Sun, 21 Jun 2020 18:06:32: 4000000 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 18:06:36: 10000000 INFO @ Sun, 21 Jun 2020 18:06:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433397/SRX1433397.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433397/SRX1433397.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433397/SRX1433397.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433397/SRX1433397.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 18:06:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:06:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:06:38: 5000000 INFO @ Sun, 21 Jun 2020 18:06:43: 11000000 INFO @ Sun, 21 Jun 2020 18:06:44: 1000000 INFO @ Sun, 21 Jun 2020 18:06:44: 6000000 INFO @ Sun, 21 Jun 2020 18:06:49: 12000000 INFO @ Sun, 21 Jun 2020 18:06:50: 2000000 INFO @ Sun, 21 Jun 2020 18:06:51: 7000000 INFO @ Sun, 21 Jun 2020 18:06:56: 13000000 INFO @ Sun, 21 Jun 2020 18:06:56: 3000000 INFO @ Sun, 21 Jun 2020 18:06:57: 8000000 INFO @ Sun, 21 Jun 2020 18:07:02: 14000000 INFO @ Sun, 21 Jun 2020 18:07:03: 4000000 INFO @ Sun, 21 Jun 2020 18:07:03: 9000000 INFO @ Sun, 21 Jun 2020 18:07:08: 15000000 INFO @ Sun, 21 Jun 2020 18:07:09: 5000000 INFO @ Sun, 21 Jun 2020 18:07:10: 10000000 INFO @ Sun, 21 Jun 2020 18:07:15: 16000000 INFO @ Sun, 21 Jun 2020 18:07:15: 6000000 INFO @ Sun, 21 Jun 2020 18:07:16: 11000000 INFO @ Sun, 21 Jun 2020 18:07:21: 17000000 INFO @ Sun, 21 Jun 2020 18:07:21: 7000000 INFO @ Sun, 21 Jun 2020 18:07:22: 12000000 INFO @ Sun, 21 Jun 2020 18:07:27: 18000000 INFO @ Sun, 21 Jun 2020 18:07:28: 8000000 INFO @ Sun, 21 Jun 2020 18:07:28: 13000000 INFO @ Sun, 21 Jun 2020 18:07:34: 19000000 INFO @ Sun, 21 Jun 2020 18:07:34: 9000000 INFO @ Sun, 21 Jun 2020 18:07:35: 14000000 INFO @ Sun, 21 Jun 2020 18:07:40: 20000000 INFO @ Sun, 21 Jun 2020 18:07:40: 10000000 INFO @ Sun, 21 Jun 2020 18:07:41: 15000000 INFO @ Sun, 21 Jun 2020 18:07:46: 21000000 INFO @ Sun, 21 Jun 2020 18:07:47: 11000000 INFO @ Sun, 21 Jun 2020 18:07:47: 16000000 INFO @ Sun, 21 Jun 2020 18:07:52: 22000000 INFO @ Sun, 21 Jun 2020 18:07:53: 12000000 INFO @ Sun, 21 Jun 2020 18:07:53: 17000000 INFO @ Sun, 21 Jun 2020 18:07:59: 23000000 INFO @ Sun, 21 Jun 2020 18:07:59: 13000000 INFO @ Sun, 21 Jun 2020 18:08:00: 18000000 INFO @ Sun, 21 Jun 2020 18:08:06: 14000000 INFO @ Sun, 21 Jun 2020 18:08:06: 24000000 INFO @ Sun, 21 Jun 2020 18:08:06: 19000000 INFO @ Sun, 21 Jun 2020 18:08:12: 15000000 INFO @ Sun, 21 Jun 2020 18:08:12: 25000000 INFO @ Sun, 21 Jun 2020 18:08:12: 20000000 INFO @ Sun, 21 Jun 2020 18:08:18: 16000000 INFO @ Sun, 21 Jun 2020 18:08:18: 26000000 INFO @ Sun, 21 Jun 2020 18:08:18: 21000000 INFO @ Sun, 21 Jun 2020 18:08:23: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:08:23: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:08:23: #1 total tags in treatment: 26588843 INFO @ Sun, 21 Jun 2020 18:08:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:08:23: #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 18:08:23: #1 tags after filtering in treatment: 26588791 INFO @ Sun, 21 Jun 2020 18:08:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:08:23: #1 finished! INFO @ Sun, 21 Jun 2020 18:08:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:08:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:08:24: 17000000 INFO @ Sun, 21 Jun 2020 18:08:25: 22000000 INFO @ Sun, 21 Jun 2020 18:08:25: #2 number of paired peaks: 456 WARNING @ Sun, 21 Jun 2020 18:08:25: Fewer paired peaks (456) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 456 pairs to build model! INFO @ Sun, 21 Jun 2020 18:08:25: start model_add_line... INFO @ Sun, 21 Jun 2020 18:08:25: start X-correlation... INFO @ Sun, 21 Jun 2020 18:08:25: end of X-cor INFO @ Sun, 21 Jun 2020 18:08:25: #2 finished! INFO @ Sun, 21 Jun 2020 18:08:25: #2 predicted fragment length is 76 bps INFO @ Sun, 21 Jun 2020 18:08:25: #2 alternative fragment length(s) may be 2,76 bps INFO @ Sun, 21 Jun 2020 18:08:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433397/SRX1433397.05_model.r WARNING @ Sun, 21 Jun 2020 18:08:25: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:08:25: #2 You may need to consider one of the other alternative d(s): 2,76 WARNING @ Sun, 21 Jun 2020 18:08:25: #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 18:08:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:08:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:08:31: 18000000 INFO @ Sun, 21 Jun 2020 18:08:31: 23000000 INFO @ Sun, 21 Jun 2020 18:08:37: 19000000 INFO @ Sun, 21 Jun 2020 18:08:37: 24000000 INFO @ Sun, 21 Jun 2020 18:08:43: 20000000 INFO @ Sun, 21 Jun 2020 18:08:44: 25000000 INFO @ Sun, 21 Jun 2020 18:08:49: 21000000 INFO @ Sun, 21 Jun 2020 18:08:50: 26000000 INFO @ Sun, 21 Jun 2020 18:08:54: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:08:54: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:08:54: #1 total tags in treatment: 26588843 INFO @ Sun, 21 Jun 2020 18:08:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:08:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:08:55: #1 tags after filtering in treatment: 26588791 INFO @ Sun, 21 Jun 2020 18:08:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:08:55: #1 finished! INFO @ Sun, 21 Jun 2020 18:08:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:08:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:08:56: 22000000 INFO @ Sun, 21 Jun 2020 18:08:57: #2 number of paired peaks: 456 WARNING @ Sun, 21 Jun 2020 18:08:57: Fewer paired peaks (456) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 456 pairs to build model! INFO @ Sun, 21 Jun 2020 18:08:57: start model_add_line... INFO @ Sun, 21 Jun 2020 18:08:57: start X-correlation... INFO @ Sun, 21 Jun 2020 18:08:57: end of X-cor INFO @ Sun, 21 Jun 2020 18:08:57: #2 finished! INFO @ Sun, 21 Jun 2020 18:08:57: #2 predicted fragment length is 76 bps INFO @ Sun, 21 Jun 2020 18:08:57: #2 alternative fragment length(s) may be 2,76 bps INFO @ Sun, 21 Jun 2020 18:08:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433397/SRX1433397.10_model.r WARNING @ Sun, 21 Jun 2020 18:08:57: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:08:57: #2 You may need to consider one of the other alternative d(s): 2,76 WARNING @ Sun, 21 Jun 2020 18:08:57: #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 18:08:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:08:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:09:02: 23000000 INFO @ Sun, 21 Jun 2020 18:09:08: 24000000 INFO @ Sun, 21 Jun 2020 18:09:14: 25000000 INFO @ Sun, 21 Jun 2020 18:09:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:09:20: 26000000 INFO @ Sun, 21 Jun 2020 18:09:24: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:09:24: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:09:24: #1 total tags in treatment: 26588843 INFO @ Sun, 21 Jun 2020 18:09:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:09:24: #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 18:09:24: #1 tags after filtering in treatment: 26588791 INFO @ Sun, 21 Jun 2020 18:09:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:09:24: #1 finished! INFO @ Sun, 21 Jun 2020 18:09:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:09:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:09:26: #2 number of paired peaks: 456 WARNING @ Sun, 21 Jun 2020 18:09:26: Fewer paired peaks (456) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 456 pairs to build model! INFO @ Sun, 21 Jun 2020 18:09:26: start model_add_line... INFO @ Sun, 21 Jun 2020 18:09:26: start X-correlation... INFO @ Sun, 21 Jun 2020 18:09:26: end of X-cor INFO @ Sun, 21 Jun 2020 18:09:26: #2 finished! INFO @ Sun, 21 Jun 2020 18:09:26: #2 predicted fragment length is 76 bps INFO @ Sun, 21 Jun 2020 18:09:26: #2 alternative fragment length(s) may be 2,76 bps INFO @ Sun, 21 Jun 2020 18:09:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433397/SRX1433397.20_model.r WARNING @ Sun, 21 Jun 2020 18:09:26: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:09:26: #2 You may need to consider one of the other alternative d(s): 2,76 WARNING @ Sun, 21 Jun 2020 18:09:26: #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 18:09:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:09:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:09:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433397/SRX1433397.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:09:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433397/SRX1433397.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:09:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433397/SRX1433397.05_summits.bed INFO @ Sun, 21 Jun 2020 18:09:41: Done! pass1 - making usageList (527 chroms): 2 millis pass2 - checking and writing primary data (3578 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:09:48: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:10:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433397/SRX1433397.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:10:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433397/SRX1433397.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:10:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433397/SRX1433397.10_summits.bed INFO @ Sun, 21 Jun 2020 18:10:12: Done! pass1 - making usageList (326 chroms): 2 millis pass2 - checking and writing primary data (1549 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:10:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:10:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433397/SRX1433397.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:10:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433397/SRX1433397.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:10:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433397/SRX1433397.20_summits.bed INFO @ Sun, 21 Jun 2020 18:10:42: Done! pass1 - making usageList (186 chroms): 1 millis pass2 - checking and writing primary data (726 records, 4 fields): 9 millis CompletedMACS2peakCalling