Job ID = 6527787 SRX = SRX287591 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:23:33 prefetch.2.10.7: 1) Downloading 'SRR869734'... 2020-06-29T13:23:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:28:50 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:28:50 prefetch.2.10.7: 1) 'SRR869734' was downloaded successfully Read 23008083 spots for SRR869734/SRR869734.sra Written 23008083 spots for SRR869734/SRR869734.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: 00:08:47 23008083 reads; of these: 23008083 (100.00%) were unpaired; of these: 1291523 (5.61%) aligned 0 times 14514891 (63.09%) aligned exactly 1 time 7201669 (31.30%) aligned >1 times 94.39% overall alignment rate Time searching: 00:08:47 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: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 3391619 / 21716560 = 0.1562 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 @ Mon, 29 Jun 2020 22:49:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287591/SRX287591.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287591/SRX287591.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287591/SRX287591.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287591/SRX287591.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 @ Mon, 29 Jun 2020 22:49:04: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:49:04: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:49:09: 1000000 INFO @ Mon, 29 Jun 2020 22:49:15: 2000000 INFO @ Mon, 29 Jun 2020 22:49:20: 3000000 INFO @ Mon, 29 Jun 2020 22:49:26: 4000000 INFO @ Mon, 29 Jun 2020 22:49:31: 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 @ Mon, 29 Jun 2020 22:49:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287591/SRX287591.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287591/SRX287591.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287591/SRX287591.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287591/SRX287591.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 @ Mon, 29 Jun 2020 22:49:34: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:49:34: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:49:37: 6000000 INFO @ Mon, 29 Jun 2020 22:49:39: 1000000 INFO @ Mon, 29 Jun 2020 22:49:42: 7000000 INFO @ Mon, 29 Jun 2020 22:49:45: 2000000 INFO @ Mon, 29 Jun 2020 22:49:48: 8000000 INFO @ Mon, 29 Jun 2020 22:49:50: 3000000 INFO @ Mon, 29 Jun 2020 22:49:53: 9000000 INFO @ Mon, 29 Jun 2020 22:49:56: 4000000 INFO @ Mon, 29 Jun 2020 22:49:58: 10000000 INFO @ Mon, 29 Jun 2020 22:50:01: 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 @ Mon, 29 Jun 2020 22:50:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287591/SRX287591.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287591/SRX287591.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287591/SRX287591.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287591/SRX287591.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 @ Mon, 29 Jun 2020 22:50:04: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:50:04: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:50:04: 11000000 INFO @ Mon, 29 Jun 2020 22:50:07: 6000000 INFO @ Mon, 29 Jun 2020 22:50:09: 12000000 INFO @ Mon, 29 Jun 2020 22:50:09: 1000000 INFO @ Mon, 29 Jun 2020 22:50:12: 7000000 INFO @ Mon, 29 Jun 2020 22:50:15: 13000000 INFO @ Mon, 29 Jun 2020 22:50:15: 2000000 INFO @ Mon, 29 Jun 2020 22:50:18: 8000000 INFO @ Mon, 29 Jun 2020 22:50:20: 14000000 INFO @ Mon, 29 Jun 2020 22:50:20: 3000000 INFO @ Mon, 29 Jun 2020 22:50:23: 9000000 INFO @ Mon, 29 Jun 2020 22:50:26: 15000000 INFO @ Mon, 29 Jun 2020 22:50:26: 4000000 INFO @ Mon, 29 Jun 2020 22:50:29: 10000000 INFO @ Mon, 29 Jun 2020 22:50:31: 16000000 INFO @ Mon, 29 Jun 2020 22:50:31: 5000000 INFO @ Mon, 29 Jun 2020 22:50:34: 11000000 INFO @ Mon, 29 Jun 2020 22:50:36: 17000000 INFO @ Mon, 29 Jun 2020 22:50:37: 6000000 INFO @ Mon, 29 Jun 2020 22:50:40: 12000000 INFO @ Mon, 29 Jun 2020 22:50:42: 18000000 INFO @ Mon, 29 Jun 2020 22:50:42: 7000000 INFO @ Mon, 29 Jun 2020 22:50:43: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:50:43: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:50:43: #1 total tags in treatment: 18324941 INFO @ Mon, 29 Jun 2020 22:50:43: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:50:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:50:44: #1 tags after filtering in treatment: 18324941 INFO @ Mon, 29 Jun 2020 22:50:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:50:44: #1 finished! INFO @ Mon, 29 Jun 2020 22:50:44: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:50:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:50:45: #2 number of paired peaks: 152 WARNING @ Mon, 29 Jun 2020 22:50:45: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Mon, 29 Jun 2020 22:50:45: start model_add_line... INFO @ Mon, 29 Jun 2020 22:50:45: start X-correlation... INFO @ Mon, 29 Jun 2020 22:50:45: end of X-cor INFO @ Mon, 29 Jun 2020 22:50:45: #2 finished! INFO @ Mon, 29 Jun 2020 22:50:45: #2 predicted fragment length is 45 bps INFO @ Mon, 29 Jun 2020 22:50:45: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 29 Jun 2020 22:50:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287591/SRX287591.05_model.r WARNING @ Mon, 29 Jun 2020 22:50:45: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:50:45: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 29 Jun 2020 22:50:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:50:45: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:50:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:50:45: 13000000 INFO @ Mon, 29 Jun 2020 22:50:48: 8000000 INFO @ Mon, 29 Jun 2020 22:50:50: 14000000 INFO @ Mon, 29 Jun 2020 22:50:53: 9000000 INFO @ Mon, 29 Jun 2020 22:50:56: 15000000 INFO @ Mon, 29 Jun 2020 22:50:59: 10000000 INFO @ Mon, 29 Jun 2020 22:51:01: 16000000 INFO @ Mon, 29 Jun 2020 22:51:04: 11000000 INFO @ Mon, 29 Jun 2020 22:51:07: 17000000 INFO @ Mon, 29 Jun 2020 22:51:10: 12000000 INFO @ Mon, 29 Jun 2020 22:51:12: 18000000 INFO @ Mon, 29 Jun 2020 22:51:14: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:51:14: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:51:14: #1 total tags in treatment: 18324941 INFO @ Mon, 29 Jun 2020 22:51:14: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:51:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:51:14: #1 tags after filtering in treatment: 18324941 INFO @ Mon, 29 Jun 2020 22:51:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:51:14: #1 finished! INFO @ Mon, 29 Jun 2020 22:51:14: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:51:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:51:15: 13000000 INFO @ Mon, 29 Jun 2020 22:51:16: #2 number of paired peaks: 152 WARNING @ Mon, 29 Jun 2020 22:51:16: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Mon, 29 Jun 2020 22:51:16: start model_add_line... INFO @ Mon, 29 Jun 2020 22:51:16: start X-correlation... INFO @ Mon, 29 Jun 2020 22:51:16: end of X-cor INFO @ Mon, 29 Jun 2020 22:51:16: #2 finished! INFO @ Mon, 29 Jun 2020 22:51:16: #2 predicted fragment length is 45 bps INFO @ Mon, 29 Jun 2020 22:51:16: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 29 Jun 2020 22:51:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287591/SRX287591.10_model.r WARNING @ Mon, 29 Jun 2020 22:51:16: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:51:16: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 29 Jun 2020 22:51:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:51:16: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:51:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:51:19: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:51:21: 14000000 INFO @ Mon, 29 Jun 2020 22:51:26: 15000000 INFO @ Mon, 29 Jun 2020 22:51:31: 16000000 INFO @ Mon, 29 Jun 2020 22:51:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287591/SRX287591.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:51:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287591/SRX287591.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:51:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287591/SRX287591.05_summits.bed INFO @ Mon, 29 Jun 2020 22:51:36: Done! INFO @ Mon, 29 Jun 2020 22:51:36: 17000000 pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2187 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:51:42: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:51:43: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:51:43: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:51:43: #1 total tags in treatment: 18324941 INFO @ Mon, 29 Jun 2020 22:51:43: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:51:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:51:44: #1 tags after filtering in treatment: 18324941 INFO @ Mon, 29 Jun 2020 22:51:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:51:44: #1 finished! INFO @ Mon, 29 Jun 2020 22:51:44: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:51:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:51:45: #2 number of paired peaks: 152 WARNING @ Mon, 29 Jun 2020 22:51:45: Fewer paired peaks (152) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 152 pairs to build model! INFO @ Mon, 29 Jun 2020 22:51:45: start model_add_line... INFO @ Mon, 29 Jun 2020 22:51:45: start X-correlation... INFO @ Mon, 29 Jun 2020 22:51:45: end of X-cor INFO @ Mon, 29 Jun 2020 22:51:45: #2 finished! INFO @ Mon, 29 Jun 2020 22:51:45: #2 predicted fragment length is 45 bps INFO @ Mon, 29 Jun 2020 22:51:45: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 29 Jun 2020 22:51:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287591/SRX287591.20_model.r WARNING @ Mon, 29 Jun 2020 22:51:45: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:51:45: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 29 Jun 2020 22:51:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:51:45: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:51:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:51:50: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:52:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287591/SRX287591.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:52:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287591/SRX287591.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:52:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287591/SRX287591.10_summits.bed INFO @ Mon, 29 Jun 2020 22:52:07: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1814 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:52:19: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:52:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287591/SRX287591.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:52:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287591/SRX287591.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:52:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287591/SRX287591.20_summits.bed INFO @ Mon, 29 Jun 2020 22:52:36: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1330 records, 4 fields): 3 millis CompletedMACS2peakCalling