Job ID = 6454645 SRX = SRX242864 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:19:24 prefetch.2.10.7: 1) Downloading 'SRR657168'... 2020-06-21T09:19:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:21:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:21:51 prefetch.2.10.7: 'SRR657168' is valid 2020-06-21T09:21:51 prefetch.2.10.7: 1) 'SRR657168' was downloaded successfully Read 11187581 spots for SRR657168/SRR657168.sra Written 11187581 spots for SRR657168/SRR657168.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: 00:01:05 11187581 reads; of these: 11187581 (100.00%) were unpaired; of these: 9522153 (85.11%) aligned 0 times 1206536 (10.78%) aligned exactly 1 time 458892 (4.10%) aligned >1 times 14.89% overall alignment rate Time searching: 00:01:05 Overall time: 00:01:05 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_rmdupse_core] 59257 / 1665428 = 0.0356 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 18:24:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX242864/SRX242864.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX242864/SRX242864.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX242864/SRX242864.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX242864/SRX242864.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 18:24:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:24:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:24:30: 1000000 INFO @ Sun, 21 Jun 2020 18:24:34: #1 tag size is determined as 35 bps INFO @ Sun, 21 Jun 2020 18:24:34: #1 tag size = 35 INFO @ Sun, 21 Jun 2020 18:24:34: #1 total tags in treatment: 1606171 INFO @ Sun, 21 Jun 2020 18:24:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:24:34: #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 18:24:35: #1 tags after filtering in treatment: 1606008 INFO @ Sun, 21 Jun 2020 18:24:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:24:35: #1 finished! INFO @ Sun, 21 Jun 2020 18:24:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:24:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:24:35: #2 number of paired peaks: 706 WARNING @ Sun, 21 Jun 2020 18:24:35: Fewer paired peaks (706) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 706 pairs to build model! INFO @ Sun, 21 Jun 2020 18:24:35: start model_add_line... INFO @ Sun, 21 Jun 2020 18:24:35: start X-correlation... INFO @ Sun, 21 Jun 2020 18:24:35: end of X-cor INFO @ Sun, 21 Jun 2020 18:24:35: #2 finished! INFO @ Sun, 21 Jun 2020 18:24:35: #2 predicted fragment length is 41 bps INFO @ Sun, 21 Jun 2020 18:24:35: #2 alternative fragment length(s) may be 41,107,193,488,535,589 bps INFO @ Sun, 21 Jun 2020 18:24:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX242864/SRX242864.05_model.r WARNING @ Sun, 21 Jun 2020 18:24:35: #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 18:24:35: #2 You may need to consider one of the other alternative d(s): 41,107,193,488,535,589 WARNING @ Sun, 21 Jun 2020 18:24:35: #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 18:24:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:24:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:24:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:24:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX242864/SRX242864.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:24:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX242864/SRX242864.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:24:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX242864/SRX242864.05_summits.bed INFO @ Sun, 21 Jun 2020 18:24:41: Done! pass1 - making usageList (337 chroms): 1 millis pass2 - checking and writing primary data (771 records, 4 fields): 12 millis CompletedMACS2peakCalling 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 18:24:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX242864/SRX242864.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX242864/SRX242864.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX242864/SRX242864.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX242864/SRX242864.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 18:24:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:24:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:24:59: 1000000 INFO @ Sun, 21 Jun 2020 18:25:03: #1 tag size is determined as 35 bps INFO @ Sun, 21 Jun 2020 18:25:03: #1 tag size = 35 INFO @ Sun, 21 Jun 2020 18:25:03: #1 total tags in treatment: 1606171 INFO @ Sun, 21 Jun 2020 18:25:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:25:03: #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 18:25:03: #1 tags after filtering in treatment: 1606008 INFO @ Sun, 21 Jun 2020 18:25:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:25:03: #1 finished! INFO @ Sun, 21 Jun 2020 18:25:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:25:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:25:03: #2 number of paired peaks: 706 WARNING @ Sun, 21 Jun 2020 18:25:03: Fewer paired peaks (706) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 706 pairs to build model! INFO @ Sun, 21 Jun 2020 18:25:03: start model_add_line... INFO @ Sun, 21 Jun 2020 18:25:03: start X-correlation... INFO @ Sun, 21 Jun 2020 18:25:03: end of X-cor INFO @ Sun, 21 Jun 2020 18:25:03: #2 finished! INFO @ Sun, 21 Jun 2020 18:25:03: #2 predicted fragment length is 41 bps INFO @ Sun, 21 Jun 2020 18:25:03: #2 alternative fragment length(s) may be 41,107,193,488,535,589 bps INFO @ Sun, 21 Jun 2020 18:25:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX242864/SRX242864.10_model.r WARNING @ Sun, 21 Jun 2020 18:25:03: #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 18:25:03: #2 You may need to consider one of the other alternative d(s): 41,107,193,488,535,589 WARNING @ Sun, 21 Jun 2020 18:25:03: #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 18:25:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:25:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:25:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:25:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX242864/SRX242864.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:25:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX242864/SRX242864.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:25:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX242864/SRX242864.10_summits.bed INFO @ Sun, 21 Jun 2020 18:25:09: Done! pass1 - making usageList (127 chroms): 1 millis pass2 - checking and writing primary data (206 records, 4 fields): 6 millis CompletedMACS2peakCalling 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 18:25:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX242864/SRX242864.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX242864/SRX242864.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX242864/SRX242864.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX242864/SRX242864.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 18:25:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:25:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:25:30: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:25:35: #1 tag size is determined as 35 bps INFO @ Sun, 21 Jun 2020 18:25:35: #1 tag size = 35 INFO @ Sun, 21 Jun 2020 18:25:35: #1 total tags in treatment: 1606171 INFO @ Sun, 21 Jun 2020 18:25:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:25:35: #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 18:25:35: #1 tags after filtering in treatment: 1606008 INFO @ Sun, 21 Jun 2020 18:25:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:25:35: #1 finished! INFO @ Sun, 21 Jun 2020 18:25:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:25:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:25:35: #2 number of paired peaks: 706 WARNING @ Sun, 21 Jun 2020 18:25:35: Fewer paired peaks (706) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 706 pairs to build model! INFO @ Sun, 21 Jun 2020 18:25:35: start model_add_line... INFO @ Sun, 21 Jun 2020 18:25:35: start X-correlation... INFO @ Sun, 21 Jun 2020 18:25:35: end of X-cor INFO @ Sun, 21 Jun 2020 18:25:35: #2 finished! INFO @ Sun, 21 Jun 2020 18:25:35: #2 predicted fragment length is 41 bps INFO @ Sun, 21 Jun 2020 18:25:35: #2 alternative fragment length(s) may be 41,107,193,488,535,589 bps INFO @ Sun, 21 Jun 2020 18:25:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX242864/SRX242864.20_model.r WARNING @ Sun, 21 Jun 2020 18:25:35: #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 18:25:35: #2 You may need to consider one of the other alternative d(s): 41,107,193,488,535,589 WARNING @ Sun, 21 Jun 2020 18:25:35: #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 18:25:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:25:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:25:39: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:25:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX242864/SRX242864.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:25:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX242864/SRX242864.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:25:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX242864/SRX242864.20_summits.bed INFO @ Sun, 21 Jun 2020 18:25:41: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (43 records, 4 fields): 2 millis CompletedMACS2peakCalling