Job ID = 6452979 SRX = SRX085400 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:07:48 prefetch.2.10.7: 1) Downloading 'SRR317178'... 2020-06-21T08:07:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:12:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:12:25 prefetch.2.10.7: 'SRR317178' is valid 2020-06-21T08:12:25 prefetch.2.10.7: 1) 'SRR317178' was downloaded successfully Read 21362116 spots for SRR317178/SRR317178.sra Written 21362116 spots for SRR317178/SRR317178.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: 00:04:29 21362116 reads; of these: 21362116 (100.00%) were unpaired; of these: 11391430 (53.33%) aligned 0 times 8506468 (39.82%) aligned exactly 1 time 1464218 (6.85%) aligned >1 times 46.67% overall alignment rate Time searching: 00:04:29 Overall time: 00:04:29 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] 6058172 / 9970686 = 0.6076 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 17:20:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX085400/SRX085400.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX085400/SRX085400.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX085400/SRX085400.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX085400/SRX085400.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 17:20:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:20:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:20:33: 1000000 INFO @ Sun, 21 Jun 2020 17:20:39: 2000000 INFO @ Sun, 21 Jun 2020 17:20:44: 3000000 INFO @ Sun, 21 Jun 2020 17:20:50: #1 tag size is determined as 54 bps INFO @ Sun, 21 Jun 2020 17:20:50: #1 tag size = 54 INFO @ Sun, 21 Jun 2020 17:20:50: #1 total tags in treatment: 3912514 INFO @ Sun, 21 Jun 2020 17:20:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:20:50: #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 17:20:50: #1 tags after filtering in treatment: 3912350 INFO @ Sun, 21 Jun 2020 17:20:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:20:50: #1 finished! INFO @ Sun, 21 Jun 2020 17:20:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:20:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:20:51: #2 number of paired peaks: 5586 INFO @ Sun, 21 Jun 2020 17:20:51: start model_add_line... INFO @ Sun, 21 Jun 2020 17:20:51: start X-correlation... INFO @ Sun, 21 Jun 2020 17:20:51: end of X-cor INFO @ Sun, 21 Jun 2020 17:20:51: #2 finished! INFO @ Sun, 21 Jun 2020 17:20:51: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 17:20:51: #2 alternative fragment length(s) may be 56 bps INFO @ Sun, 21 Jun 2020 17:20:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX085400/SRX085400.05_model.r WARNING @ Sun, 21 Jun 2020 17:20:51: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:20:51: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Sun, 21 Jun 2020 17:20:51: #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 17:20:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:20:51: #3 Pre-compute pvalue-qvalue table... 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 17:20:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX085400/SRX085400.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX085400/SRX085400.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX085400/SRX085400.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX085400/SRX085400.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 17:20:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:20:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:21:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:21:03: 1000000 INFO @ Sun, 21 Jun 2020 17:21:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX085400/SRX085400.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:21:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX085400/SRX085400.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:21:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX085400/SRX085400.05_summits.bed INFO @ Sun, 21 Jun 2020 17:21:05: Done! pass1 - making usageList (503 chroms): 2 millis pass2 - checking and writing primary data (10932 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:21:10: 2000000 INFO @ Sun, 21 Jun 2020 17:21:16: 3000000 INFO @ Sun, 21 Jun 2020 17:21:22: #1 tag size is determined as 54 bps INFO @ Sun, 21 Jun 2020 17:21:22: #1 tag size = 54 INFO @ Sun, 21 Jun 2020 17:21:22: #1 total tags in treatment: 3912514 INFO @ Sun, 21 Jun 2020 17:21:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:21:22: #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 17:21:22: #1 tags after filtering in treatment: 3912350 INFO @ Sun, 21 Jun 2020 17:21:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:21:22: #1 finished! INFO @ Sun, 21 Jun 2020 17:21:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:21:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:21:23: #2 number of paired peaks: 5586 INFO @ Sun, 21 Jun 2020 17:21:23: start model_add_line... INFO @ Sun, 21 Jun 2020 17:21:23: start X-correlation... INFO @ Sun, 21 Jun 2020 17:21:23: end of X-cor INFO @ Sun, 21 Jun 2020 17:21:23: #2 finished! INFO @ Sun, 21 Jun 2020 17:21:23: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 17:21:23: #2 alternative fragment length(s) may be 56 bps INFO @ Sun, 21 Jun 2020 17:21:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX085400/SRX085400.10_model.r WARNING @ Sun, 21 Jun 2020 17:21:23: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:21:23: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Sun, 21 Jun 2020 17:21:23: #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 17:21:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:21:23: #3 Pre-compute pvalue-qvalue table... 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 17:21:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX085400/SRX085400.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX085400/SRX085400.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX085400/SRX085400.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX085400/SRX085400.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 17:21:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:21:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:21:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:21:33: 1000000 INFO @ Sun, 21 Jun 2020 17:21:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX085400/SRX085400.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:21:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX085400/SRX085400.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:21:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX085400/SRX085400.10_summits.bed INFO @ Sun, 21 Jun 2020 17:21:37: Done! pass1 - making usageList (288 chroms): 2 millis pass2 - checking and writing primary data (8265 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:21:39: 2000000 INFO @ Sun, 21 Jun 2020 17:21:44: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:21:50: #1 tag size is determined as 54 bps INFO @ Sun, 21 Jun 2020 17:21:50: #1 tag size = 54 INFO @ Sun, 21 Jun 2020 17:21:50: #1 total tags in treatment: 3912514 INFO @ Sun, 21 Jun 2020 17:21:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:21:50: #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 17:21:50: #1 tags after filtering in treatment: 3912350 INFO @ Sun, 21 Jun 2020 17:21:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:21:50: #1 finished! INFO @ Sun, 21 Jun 2020 17:21:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:21:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:21:51: #2 number of paired peaks: 5586 INFO @ Sun, 21 Jun 2020 17:21:51: start model_add_line... INFO @ Sun, 21 Jun 2020 17:21:51: start X-correlation... INFO @ Sun, 21 Jun 2020 17:21:51: end of X-cor INFO @ Sun, 21 Jun 2020 17:21:51: #2 finished! INFO @ Sun, 21 Jun 2020 17:21:51: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 17:21:51: #2 alternative fragment length(s) may be 56 bps INFO @ Sun, 21 Jun 2020 17:21:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX085400/SRX085400.20_model.r WARNING @ Sun, 21 Jun 2020 17:21:51: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:21:51: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Sun, 21 Jun 2020 17:21:51: #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 17:21:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:21:51: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:22:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:22:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX085400/SRX085400.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:22:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX085400/SRX085400.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:22:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX085400/SRX085400.20_summits.bed INFO @ Sun, 21 Jun 2020 17:22:05: Done! pass1 - making usageList (189 chroms): 2 millis pass2 - checking and writing primary data (5934 records, 4 fields): 14 millis CompletedMACS2peakCalling