Job ID = 6508477 SRX = SRX287899 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:23:14 prefetch.2.10.7: 1) Downloading 'SRR870088'... 2020-06-26T14:23:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:26:22 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:26:22 prefetch.2.10.7: 'SRR870088' is valid 2020-06-26T14:26:22 prefetch.2.10.7: 1) 'SRR870088' was downloaded successfully Read 11858412 spots for SRR870088/SRR870088.sra Written 11858412 spots for SRR870088/SRR870088.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: 00:04:23 11858412 reads; of these: 11858412 (100.00%) were unpaired; of these: 560997 (4.73%) aligned 0 times 8313821 (70.11%) aligned exactly 1 time 2983594 (25.16%) aligned >1 times 95.27% overall alignment rate Time searching: 00:04:23 Overall time: 00:04:23 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] 1355736 / 11297415 = 0.1200 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 @ Fri, 26 Jun 2020 23:35:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287899/SRX287899.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287899/SRX287899.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287899/SRX287899.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287899/SRX287899.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 @ Fri, 26 Jun 2020 23:35:17: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:35:17: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:35:23: 1000000 INFO @ Fri, 26 Jun 2020 23:35:30: 2000000 INFO @ Fri, 26 Jun 2020 23:35:36: 3000000 INFO @ Fri, 26 Jun 2020 23:35:42: 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 @ Fri, 26 Jun 2020 23:35:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287899/SRX287899.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287899/SRX287899.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287899/SRX287899.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287899/SRX287899.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 @ Fri, 26 Jun 2020 23:35:47: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:35:47: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:35:49: 5000000 INFO @ Fri, 26 Jun 2020 23:35:54: 1000000 INFO @ Fri, 26 Jun 2020 23:35:55: 6000000 INFO @ Fri, 26 Jun 2020 23:36:01: 2000000 INFO @ Fri, 26 Jun 2020 23:36:01: 7000000 INFO @ Fri, 26 Jun 2020 23:36:07: 3000000 INFO @ Fri, 26 Jun 2020 23:36:08: 8000000 INFO @ Fri, 26 Jun 2020 23:36:14: 4000000 INFO @ Fri, 26 Jun 2020 23:36:15: 9000000 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 @ Fri, 26 Jun 2020 23:36:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287899/SRX287899.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287899/SRX287899.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287899/SRX287899.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287899/SRX287899.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 @ Fri, 26 Jun 2020 23:36:17: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:36:17: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:36:20: 5000000 INFO @ Fri, 26 Jun 2020 23:36:21: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:36:21: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:36:21: #1 total tags in treatment: 9941679 INFO @ Fri, 26 Jun 2020 23:36:21: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:36:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:36:22: #1 tags after filtering in treatment: 9941674 INFO @ Fri, 26 Jun 2020 23:36:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:36:22: #1 finished! INFO @ Fri, 26 Jun 2020 23:36:22: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:36:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:36:22: #2 number of paired peaks: 394 WARNING @ Fri, 26 Jun 2020 23:36:22: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Fri, 26 Jun 2020 23:36:22: start model_add_line... INFO @ Fri, 26 Jun 2020 23:36:22: start X-correlation... INFO @ Fri, 26 Jun 2020 23:36:22: end of X-cor INFO @ Fri, 26 Jun 2020 23:36:22: #2 finished! INFO @ Fri, 26 Jun 2020 23:36:22: #2 predicted fragment length is 67 bps INFO @ Fri, 26 Jun 2020 23:36:22: #2 alternative fragment length(s) may be 67 bps INFO @ Fri, 26 Jun 2020 23:36:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287899/SRX287899.05_model.r WARNING @ Fri, 26 Jun 2020 23:36:22: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:36:22: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Fri, 26 Jun 2020 23:36:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:36:22: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:36:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:36:23: 1000000 INFO @ Fri, 26 Jun 2020 23:36:26: 6000000 INFO @ Fri, 26 Jun 2020 23:36:30: 2000000 INFO @ Fri, 26 Jun 2020 23:36:33: 7000000 INFO @ Fri, 26 Jun 2020 23:36:36: 3000000 INFO @ Fri, 26 Jun 2020 23:36:39: 8000000 INFO @ Fri, 26 Jun 2020 23:36:42: 4000000 INFO @ Fri, 26 Jun 2020 23:36:46: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:36:46: 9000000 INFO @ Fri, 26 Jun 2020 23:36:49: 5000000 INFO @ Fri, 26 Jun 2020 23:36:52: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:36:52: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:36:52: #1 total tags in treatment: 9941679 INFO @ Fri, 26 Jun 2020 23:36:52: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:36:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:36:52: #1 tags after filtering in treatment: 9941674 INFO @ Fri, 26 Jun 2020 23:36:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:36:52: #1 finished! INFO @ Fri, 26 Jun 2020 23:36:52: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:36:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:36:53: #2 number of paired peaks: 394 WARNING @ Fri, 26 Jun 2020 23:36:53: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Fri, 26 Jun 2020 23:36:53: start model_add_line... INFO @ Fri, 26 Jun 2020 23:36:53: start X-correlation... INFO @ Fri, 26 Jun 2020 23:36:53: end of X-cor INFO @ Fri, 26 Jun 2020 23:36:53: #2 finished! INFO @ Fri, 26 Jun 2020 23:36:53: #2 predicted fragment length is 67 bps INFO @ Fri, 26 Jun 2020 23:36:53: #2 alternative fragment length(s) may be 67 bps INFO @ Fri, 26 Jun 2020 23:36:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287899/SRX287899.10_model.r WARNING @ Fri, 26 Jun 2020 23:36:53: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:36:53: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Fri, 26 Jun 2020 23:36:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:36:53: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:36:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:36:55: 6000000 INFO @ Fri, 26 Jun 2020 23:36:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287899/SRX287899.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:36:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287899/SRX287899.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:36:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287899/SRX287899.05_summits.bed INFO @ Fri, 26 Jun 2020 23:36:58: Done! pass1 - making usageList (621 chroms): 2 millis pass2 - checking and writing primary data (2488 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:37:01: 7000000 INFO @ Fri, 26 Jun 2020 23:37:07: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:37:13: 9000000 INFO @ Fri, 26 Jun 2020 23:37:17: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:37:19: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:37:19: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:37:19: #1 total tags in treatment: 9941679 INFO @ Fri, 26 Jun 2020 23:37:19: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:37:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:37:19: #1 tags after filtering in treatment: 9941674 INFO @ Fri, 26 Jun 2020 23:37:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:37:19: #1 finished! INFO @ Fri, 26 Jun 2020 23:37:19: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:37:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:37:20: #2 number of paired peaks: 394 WARNING @ Fri, 26 Jun 2020 23:37:20: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Fri, 26 Jun 2020 23:37:20: start model_add_line... INFO @ Fri, 26 Jun 2020 23:37:20: start X-correlation... INFO @ Fri, 26 Jun 2020 23:37:20: end of X-cor INFO @ Fri, 26 Jun 2020 23:37:20: #2 finished! INFO @ Fri, 26 Jun 2020 23:37:20: #2 predicted fragment length is 67 bps INFO @ Fri, 26 Jun 2020 23:37:20: #2 alternative fragment length(s) may be 67 bps INFO @ Fri, 26 Jun 2020 23:37:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287899/SRX287899.20_model.r WARNING @ Fri, 26 Jun 2020 23:37:20: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:37:20: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Fri, 26 Jun 2020 23:37:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:37:20: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:37:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:37:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287899/SRX287899.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:37:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287899/SRX287899.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:37:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287899/SRX287899.10_summits.bed INFO @ Fri, 26 Jun 2020 23:37:28: Done! pass1 - making usageList (446 chroms): 1 millis pass2 - checking and writing primary data (1149 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:37:43: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:37:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287899/SRX287899.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:37:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287899/SRX287899.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:37:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287899/SRX287899.20_summits.bed INFO @ Fri, 26 Jun 2020 23:37:55: Done! pass1 - making usageList (169 chroms): 1 millis pass2 - checking and writing primary data (339 records, 4 fields): 7 millis CompletedMACS2peakCalling