Job ID = 6529766 SRX = SRX474569 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:03:06 12597078 reads; of these: 12597078 (100.00%) were unpaired; of these: 1780710 (14.14%) aligned 0 times 8335253 (66.17%) aligned exactly 1 time 2481115 (19.70%) aligned >1 times 85.86% overall alignment rate Time searching: 00:03:06 Overall time: 00:03:06 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] 2093806 / 10816368 = 0.1936 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 @ Tue, 30 Jun 2020 02:49:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX474569/SRX474569.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX474569/SRX474569.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX474569/SRX474569.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX474569/SRX474569.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 @ Tue, 30 Jun 2020 02:49:23: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:49:23: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:49:28: 1000000 INFO @ Tue, 30 Jun 2020 02:49:33: 2000000 INFO @ Tue, 30 Jun 2020 02:49:38: 3000000 INFO @ Tue, 30 Jun 2020 02:49:43: 4000000 INFO @ Tue, 30 Jun 2020 02:49:47: 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 @ Tue, 30 Jun 2020 02:49:52: 6000000 INFO @ Tue, 30 Jun 2020 02:49:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX474569/SRX474569.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX474569/SRX474569.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX474569/SRX474569.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX474569/SRX474569.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 @ Tue, 30 Jun 2020 02:49:53: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:49:53: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:49:57: 7000000 INFO @ Tue, 30 Jun 2020 02:49:59: 1000000 INFO @ Tue, 30 Jun 2020 02:50:02: 8000000 INFO @ Tue, 30 Jun 2020 02:50:05: 2000000 INFO @ Tue, 30 Jun 2020 02:50:06: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:50:06: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:50:06: #1 total tags in treatment: 8722562 INFO @ Tue, 30 Jun 2020 02:50:06: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:50:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:50:07: #1 tags after filtering in treatment: 8722555 INFO @ Tue, 30 Jun 2020 02:50:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:50:07: #1 finished! INFO @ Tue, 30 Jun 2020 02:50:07: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:50:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:50:07: #2 number of paired peaks: 117 WARNING @ Tue, 30 Jun 2020 02:50:07: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Tue, 30 Jun 2020 02:50:07: start model_add_line... INFO @ Tue, 30 Jun 2020 02:50:07: start X-correlation... INFO @ Tue, 30 Jun 2020 02:50:07: end of X-cor INFO @ Tue, 30 Jun 2020 02:50:07: #2 finished! INFO @ Tue, 30 Jun 2020 02:50:07: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 02:50:07: #2 alternative fragment length(s) may be 4,50,64,572 bps INFO @ Tue, 30 Jun 2020 02:50:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX474569/SRX474569.05_model.r WARNING @ Tue, 30 Jun 2020 02:50:07: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:50:07: #2 You may need to consider one of the other alternative d(s): 4,50,64,572 WARNING @ Tue, 30 Jun 2020 02:50:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:50:07: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:50:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:50:10: 3000000 INFO @ Tue, 30 Jun 2020 02:50:16: 4000000 INFO @ Tue, 30 Jun 2020 02:50:21: 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 @ Tue, 30 Jun 2020 02:50:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX474569/SRX474569.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX474569/SRX474569.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX474569/SRX474569.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX474569/SRX474569.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 @ Tue, 30 Jun 2020 02:50:23: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:50:23: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:50:25: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:50:27: 6000000 INFO @ Tue, 30 Jun 2020 02:50:28: 1000000 INFO @ Tue, 30 Jun 2020 02:50:32: 7000000 INFO @ Tue, 30 Jun 2020 02:50:33: 2000000 INFO @ Tue, 30 Jun 2020 02:50:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX474569/SRX474569.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:50:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX474569/SRX474569.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:50:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX474569/SRX474569.05_summits.bed INFO @ Tue, 30 Jun 2020 02:50:33: Done! pass1 - making usageList (222 chroms): 0 millis pass2 - checking and writing primary data (464 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:50:38: 3000000 INFO @ Tue, 30 Jun 2020 02:50:38: 8000000 INFO @ Tue, 30 Jun 2020 02:50:43: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:50:43: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:50:43: #1 total tags in treatment: 8722562 INFO @ Tue, 30 Jun 2020 02:50:43: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:50:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:50:43: 4000000 INFO @ Tue, 30 Jun 2020 02:50:43: #1 tags after filtering in treatment: 8722555 INFO @ Tue, 30 Jun 2020 02:50:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:50:43: #1 finished! INFO @ Tue, 30 Jun 2020 02:50:43: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:50:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:50:44: #2 number of paired peaks: 117 WARNING @ Tue, 30 Jun 2020 02:50:44: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Tue, 30 Jun 2020 02:50:44: start model_add_line... INFO @ Tue, 30 Jun 2020 02:50:44: start X-correlation... INFO @ Tue, 30 Jun 2020 02:50:44: end of X-cor INFO @ Tue, 30 Jun 2020 02:50:44: #2 finished! INFO @ Tue, 30 Jun 2020 02:50:44: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 02:50:44: #2 alternative fragment length(s) may be 4,50,64,572 bps INFO @ Tue, 30 Jun 2020 02:50:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX474569/SRX474569.10_model.r WARNING @ Tue, 30 Jun 2020 02:50:44: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:50:44: #2 You may need to consider one of the other alternative d(s): 4,50,64,572 WARNING @ Tue, 30 Jun 2020 02:50:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:50:44: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:50:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:50:48: 5000000 INFO @ Tue, 30 Jun 2020 02:50:53: 6000000 INFO @ Tue, 30 Jun 2020 02:50:57: 7000000 INFO @ Tue, 30 Jun 2020 02:51:01: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:51:03: 8000000 INFO @ Tue, 30 Jun 2020 02:51:06: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:51:06: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:51:06: #1 total tags in treatment: 8722562 INFO @ Tue, 30 Jun 2020 02:51:06: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:51:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:51:07: #1 tags after filtering in treatment: 8722555 INFO @ Tue, 30 Jun 2020 02:51:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:51:07: #1 finished! INFO @ Tue, 30 Jun 2020 02:51:07: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:51:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:51:07: #2 number of paired peaks: 117 WARNING @ Tue, 30 Jun 2020 02:51:07: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Tue, 30 Jun 2020 02:51:07: start model_add_line... INFO @ Tue, 30 Jun 2020 02:51:07: start X-correlation... INFO @ Tue, 30 Jun 2020 02:51:07: end of X-cor INFO @ Tue, 30 Jun 2020 02:51:07: #2 finished! INFO @ Tue, 30 Jun 2020 02:51:07: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 02:51:07: #2 alternative fragment length(s) may be 4,50,64,572 bps INFO @ Tue, 30 Jun 2020 02:51:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX474569/SRX474569.20_model.r WARNING @ Tue, 30 Jun 2020 02:51:07: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:51:07: #2 You may need to consider one of the other alternative d(s): 4,50,64,572 WARNING @ Tue, 30 Jun 2020 02:51:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:51:07: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:51:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:51:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX474569/SRX474569.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:51:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX474569/SRX474569.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:51:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX474569/SRX474569.10_summits.bed INFO @ Tue, 30 Jun 2020 02:51:10: Done! pass1 - making usageList (93 chroms): 1 millis pass2 - checking and writing primary data (200 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:51:25: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:51:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX474569/SRX474569.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:51:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX474569/SRX474569.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:51:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX474569/SRX474569.20_summits.bed INFO @ Tue, 30 Jun 2020 02:51:33: Done! pass1 - making usageList (51 chroms): 1 millis pass2 - checking and writing primary data (82 records, 4 fields): 3 millis CompletedMACS2peakCalling