Job ID = 6455691 SRX = SRX287992 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:15:21 prefetch.2.10.7: 1) Downloading 'SRR870181'... 2020-06-21T10:15:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:19:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:19:41 prefetch.2.10.7: 1) 'SRR870181' was downloaded successfully Read 17857991 spots for SRR870181/SRR870181.sra Written 17857991 spots for SRR870181/SRR870181.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: 00:05:58 17857991 reads; of these: 17857991 (100.00%) were unpaired; of these: 1028383 (5.76%) aligned 0 times 11447583 (64.10%) aligned exactly 1 time 5382025 (30.14%) aligned >1 times 94.24% overall alignment rate Time searching: 00:05:58 Overall time: 00:05:58 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] 2379875 / 16829608 = 0.1414 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 19:32:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287992/SRX287992.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287992/SRX287992.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287992/SRX287992.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287992/SRX287992.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 19:32:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:32:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:32:29: 1000000 INFO @ Sun, 21 Jun 2020 19:32:34: 2000000 INFO @ Sun, 21 Jun 2020 19:32:40: 3000000 INFO @ Sun, 21 Jun 2020 19:32:45: 4000000 INFO @ Sun, 21 Jun 2020 19:32:51: 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 19:32:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287992/SRX287992.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287992/SRX287992.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287992/SRX287992.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287992/SRX287992.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 19:32:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:32:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:32:56: 6000000 INFO @ Sun, 21 Jun 2020 19:33:00: 1000000 INFO @ Sun, 21 Jun 2020 19:33:02: 7000000 INFO @ Sun, 21 Jun 2020 19:33:06: 2000000 INFO @ Sun, 21 Jun 2020 19:33:08: 8000000 INFO @ Sun, 21 Jun 2020 19:33:12: 3000000 INFO @ Sun, 21 Jun 2020 19:33:14: 9000000 INFO @ Sun, 21 Jun 2020 19:33:18: 4000000 INFO @ Sun, 21 Jun 2020 19:33:20: 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 19:33:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287992/SRX287992.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287992/SRX287992.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287992/SRX287992.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287992/SRX287992.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 19:33:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:33:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:33:24: 5000000 INFO @ Sun, 21 Jun 2020 19:33:26: 11000000 INFO @ Sun, 21 Jun 2020 19:33:29: 1000000 INFO @ Sun, 21 Jun 2020 19:33:30: 6000000 INFO @ Sun, 21 Jun 2020 19:33:33: 12000000 INFO @ Sun, 21 Jun 2020 19:33:35: 2000000 INFO @ Sun, 21 Jun 2020 19:33:36: 7000000 INFO @ Sun, 21 Jun 2020 19:33:39: 13000000 INFO @ Sun, 21 Jun 2020 19:33:41: 3000000 INFO @ Sun, 21 Jun 2020 19:33:42: 8000000 INFO @ Sun, 21 Jun 2020 19:33:46: 14000000 INFO @ Sun, 21 Jun 2020 19:33:46: 4000000 INFO @ Sun, 21 Jun 2020 19:33:48: 9000000 INFO @ Sun, 21 Jun 2020 19:33:49: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:33:49: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:33:49: #1 total tags in treatment: 14449733 INFO @ Sun, 21 Jun 2020 19:33:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:33:49: #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 19:33:49: #1 tags after filtering in treatment: 14449733 INFO @ Sun, 21 Jun 2020 19:33:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:33:49: #1 finished! INFO @ Sun, 21 Jun 2020 19:33:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:33:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:33:50: #2 number of paired peaks: 759 WARNING @ Sun, 21 Jun 2020 19:33:50: Fewer paired peaks (759) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 759 pairs to build model! INFO @ Sun, 21 Jun 2020 19:33:50: start model_add_line... INFO @ Sun, 21 Jun 2020 19:33:51: start X-correlation... INFO @ Sun, 21 Jun 2020 19:33:51: end of X-cor INFO @ Sun, 21 Jun 2020 19:33:51: #2 finished! INFO @ Sun, 21 Jun 2020 19:33:51: #2 predicted fragment length is 41 bps INFO @ Sun, 21 Jun 2020 19:33:51: #2 alternative fragment length(s) may be 3,41 bps INFO @ Sun, 21 Jun 2020 19:33:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287992/SRX287992.05_model.r WARNING @ Sun, 21 Jun 2020 19:33:51: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:33:51: #2 You may need to consider one of the other alternative d(s): 3,41 WARNING @ Sun, 21 Jun 2020 19:33:51: #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 19:33:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:33:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:33:52: 5000000 INFO @ Sun, 21 Jun 2020 19:33:53: 10000000 INFO @ Sun, 21 Jun 2020 19:33:58: 6000000 INFO @ Sun, 21 Jun 2020 19:33:59: 11000000 INFO @ Sun, 21 Jun 2020 19:34:03: 7000000 INFO @ Sun, 21 Jun 2020 19:34:06: 12000000 INFO @ Sun, 21 Jun 2020 19:34:09: 8000000 INFO @ Sun, 21 Jun 2020 19:34:11: 13000000 INFO @ Sun, 21 Jun 2020 19:34:15: 9000000 INFO @ Sun, 21 Jun 2020 19:34:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:34:17: 14000000 INFO @ Sun, 21 Jun 2020 19:34:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:34:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:34:20: #1 total tags in treatment: 14449733 INFO @ Sun, 21 Jun 2020 19:34:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:34:20: #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 19:34:21: #1 tags after filtering in treatment: 14449733 INFO @ Sun, 21 Jun 2020 19:34:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:34:21: #1 finished! INFO @ Sun, 21 Jun 2020 19:34:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:34:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:34:21: 10000000 INFO @ Sun, 21 Jun 2020 19:34:22: #2 number of paired peaks: 759 WARNING @ Sun, 21 Jun 2020 19:34:22: Fewer paired peaks (759) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 759 pairs to build model! INFO @ Sun, 21 Jun 2020 19:34:22: start model_add_line... INFO @ Sun, 21 Jun 2020 19:34:22: start X-correlation... INFO @ Sun, 21 Jun 2020 19:34:22: end of X-cor INFO @ Sun, 21 Jun 2020 19:34:22: #2 finished! INFO @ Sun, 21 Jun 2020 19:34:22: #2 predicted fragment length is 41 bps INFO @ Sun, 21 Jun 2020 19:34:22: #2 alternative fragment length(s) may be 3,41 bps INFO @ Sun, 21 Jun 2020 19:34:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287992/SRX287992.10_model.r WARNING @ Sun, 21 Jun 2020 19:34:22: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:34:22: #2 You may need to consider one of the other alternative d(s): 3,41 WARNING @ Sun, 21 Jun 2020 19:34:22: #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 19:34:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:34:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:34:27: 11000000 INFO @ Sun, 21 Jun 2020 19:34:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287992/SRX287992.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:34:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287992/SRX287992.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:34:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287992/SRX287992.05_summits.bed INFO @ Sun, 21 Jun 2020 19:34:28: Done! pass1 - making usageList (649 chroms): 1 millis pass2 - checking and writing primary data (2377 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:34:34: 12000000 INFO @ Sun, 21 Jun 2020 19:34:39: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:34:45: 14000000 INFO @ Sun, 21 Jun 2020 19:34:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:34:48: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:34:48: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:34:48: #1 total tags in treatment: 14449733 INFO @ Sun, 21 Jun 2020 19:34:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:34:48: #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 19:34:49: #1 tags after filtering in treatment: 14449733 INFO @ Sun, 21 Jun 2020 19:34:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:34:49: #1 finished! INFO @ Sun, 21 Jun 2020 19:34:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:34:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:34:50: #2 number of paired peaks: 759 WARNING @ Sun, 21 Jun 2020 19:34:50: Fewer paired peaks (759) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 759 pairs to build model! INFO @ Sun, 21 Jun 2020 19:34:50: start model_add_line... INFO @ Sun, 21 Jun 2020 19:34:50: start X-correlation... INFO @ Sun, 21 Jun 2020 19:34:50: end of X-cor INFO @ Sun, 21 Jun 2020 19:34:50: #2 finished! INFO @ Sun, 21 Jun 2020 19:34:50: #2 predicted fragment length is 41 bps INFO @ Sun, 21 Jun 2020 19:34:50: #2 alternative fragment length(s) may be 3,41 bps INFO @ Sun, 21 Jun 2020 19:34:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287992/SRX287992.20_model.r WARNING @ Sun, 21 Jun 2020 19:34:50: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:34:50: #2 You may need to consider one of the other alternative d(s): 3,41 WARNING @ Sun, 21 Jun 2020 19:34:50: #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 19:34:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:34:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:35:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287992/SRX287992.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:35:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287992/SRX287992.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:35:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287992/SRX287992.10_summits.bed INFO @ Sun, 21 Jun 2020 19:35:00: Done! pass1 - making usageList (529 chroms): 1 millis pass2 - checking and writing primary data (2022 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:35:16: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:35:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287992/SRX287992.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:35:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287992/SRX287992.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:35:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287992/SRX287992.20_summits.bed INFO @ Sun, 21 Jun 2020 19:35:29: Done! pass1 - making usageList (421 chroms): 2 millis pass2 - checking and writing primary data (1192 records, 4 fields): 24 millis CompletedMACS2peakCalling