Job ID = 6452957 SRX = SRX066245 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:03:23 prefetch.2.10.7: 1) Downloading 'SRR222072'... 2020-06-21T08:03:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:04:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:04:56 prefetch.2.10.7: 'SRR222072' is valid 2020-06-21T08:04:56 prefetch.2.10.7: 1) 'SRR222072' was downloaded successfully Read 18552417 spots for SRR222072/SRR222072.sra Written 18552417 spots for SRR222072/SRR222072.sra 2020-06-21T08:05:54 prefetch.2.10.7: 1) Downloading 'SRR222073'... 2020-06-21T08:05:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:06:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:06:55 prefetch.2.10.7: 'SRR222073' is valid 2020-06-21T08:06:55 prefetch.2.10.7: 1) 'SRR222073' was downloaded successfully Read 5537830 spots for SRR222073/SRR222073.sra Written 5537830 spots for SRR222073/SRR222073.sra 2020-06-21T08:07:24 prefetch.2.10.7: 1) Downloading 'SRR222074'... 2020-06-21T08:07:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:08:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:08:53 prefetch.2.10.7: 'SRR222074' is valid 2020-06-21T08:08:53 prefetch.2.10.7: 1) 'SRR222074' was downloaded successfully Read 19852318 spots for SRR222074/SRR222074.sra Written 19852318 spots for SRR222074/SRR222074.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:21 43942565 reads; of these: 43942565 (100.00%) were unpaired; of these: 16369849 (37.25%) aligned 0 times 20507207 (46.67%) aligned exactly 1 time 7065509 (16.08%) aligned >1 times 62.75% overall alignment rate Time searching: 00:08:22 Overall time: 00:08:22 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] 20591365 / 27572716 = 0.7468 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 17:22:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX066245/SRX066245.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX066245/SRX066245.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX066245/SRX066245.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX066245/SRX066245.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 17:22:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:22:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:22:39: 1000000 INFO @ Sun, 21 Jun 2020 17:22:45: 2000000 INFO @ Sun, 21 Jun 2020 17:22:50: 3000000 INFO @ Sun, 21 Jun 2020 17:22:56: 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 @ Sun, 21 Jun 2020 17:23:03: 5000000 INFO @ Sun, 21 Jun 2020 17:23:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX066245/SRX066245.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX066245/SRX066245.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX066245/SRX066245.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX066245/SRX066245.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 17:23:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:23:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:23:09: 6000000 INFO @ Sun, 21 Jun 2020 17:23:10: 1000000 INFO @ Sun, 21 Jun 2020 17:23:16: 2000000 INFO @ Sun, 21 Jun 2020 17:23:16: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:23:16: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:23:16: #1 total tags in treatment: 6981351 INFO @ Sun, 21 Jun 2020 17:23:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:23:16: #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 17:23:16: #1 tags after filtering in treatment: 6981350 INFO @ Sun, 21 Jun 2020 17:23:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:23:16: #1 finished! INFO @ Sun, 21 Jun 2020 17:23:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:23:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:23:17: #2 number of paired peaks: 1799 INFO @ Sun, 21 Jun 2020 17:23:17: start model_add_line... INFO @ Sun, 21 Jun 2020 17:23:17: start X-correlation... INFO @ Sun, 21 Jun 2020 17:23:17: end of X-cor INFO @ Sun, 21 Jun 2020 17:23:17: #2 finished! INFO @ Sun, 21 Jun 2020 17:23:17: #2 predicted fragment length is 41 bps INFO @ Sun, 21 Jun 2020 17:23:17: #2 alternative fragment length(s) may be 3,41 bps INFO @ Sun, 21 Jun 2020 17:23:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX066245/SRX066245.05_model.r WARNING @ Sun, 21 Jun 2020 17:23:17: #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 17:23:17: #2 You may need to consider one of the other alternative d(s): 3,41 WARNING @ Sun, 21 Jun 2020 17:23:17: #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 17:23:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:23:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:23:21: 3000000 INFO @ Sun, 21 Jun 2020 17:23:27: 4000000 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 17:23:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:23:32: 5000000 INFO @ Sun, 21 Jun 2020 17:23:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX066245/SRX066245.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX066245/SRX066245.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX066245/SRX066245.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX066245/SRX066245.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 17:23:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:23:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:23:38: 6000000 INFO @ Sun, 21 Jun 2020 17:23:39: 1000000 INFO @ Sun, 21 Jun 2020 17:23:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX066245/SRX066245.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:23:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX066245/SRX066245.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:23:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX066245/SRX066245.05_summits.bed INFO @ Sun, 21 Jun 2020 17:23:40: Done! pass1 - making usageList (800 chroms): 2 millis pass2 - checking and writing primary data (3572 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:23:44: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:23:44: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:23:44: #1 total tags in treatment: 6981351 INFO @ Sun, 21 Jun 2020 17:23:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:23:44: #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 17:23:44: #1 tags after filtering in treatment: 6981350 INFO @ Sun, 21 Jun 2020 17:23:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:23:44: #1 finished! INFO @ Sun, 21 Jun 2020 17:23:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:23:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:23:45: #2 number of paired peaks: 1799 INFO @ Sun, 21 Jun 2020 17:23:45: start model_add_line... INFO @ Sun, 21 Jun 2020 17:23:45: 2000000 INFO @ Sun, 21 Jun 2020 17:23:45: start X-correlation... INFO @ Sun, 21 Jun 2020 17:23:45: end of X-cor INFO @ Sun, 21 Jun 2020 17:23:45: #2 finished! INFO @ Sun, 21 Jun 2020 17:23:45: #2 predicted fragment length is 41 bps INFO @ Sun, 21 Jun 2020 17:23:45: #2 alternative fragment length(s) may be 3,41 bps INFO @ Sun, 21 Jun 2020 17:23:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX066245/SRX066245.10_model.r WARNING @ Sun, 21 Jun 2020 17:23:45: #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 17:23:45: #2 You may need to consider one of the other alternative d(s): 3,41 WARNING @ Sun, 21 Jun 2020 17:23:45: #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 17:23:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:23:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:23:51: 3000000 INFO @ Sun, 21 Jun 2020 17:23:57: 4000000 INFO @ Sun, 21 Jun 2020 17:24:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:24:03: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:24:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX066245/SRX066245.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:24:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX066245/SRX066245.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:24:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX066245/SRX066245.10_summits.bed INFO @ Sun, 21 Jun 2020 17:24:07: Done! pass1 - making usageList (596 chroms): 1 millis pass2 - checking and writing primary data (2561 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:24:10: 6000000 INFO @ Sun, 21 Jun 2020 17:24:16: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 17:24:16: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 17:24:16: #1 total tags in treatment: 6981351 INFO @ Sun, 21 Jun 2020 17:24:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:24:16: #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 17:24:16: #1 tags after filtering in treatment: 6981350 INFO @ Sun, 21 Jun 2020 17:24:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:24:16: #1 finished! INFO @ Sun, 21 Jun 2020 17:24:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:24:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:24:17: #2 number of paired peaks: 1799 INFO @ Sun, 21 Jun 2020 17:24:17: start model_add_line... INFO @ Sun, 21 Jun 2020 17:24:17: start X-correlation... INFO @ Sun, 21 Jun 2020 17:24:17: end of X-cor INFO @ Sun, 21 Jun 2020 17:24:17: #2 finished! INFO @ Sun, 21 Jun 2020 17:24:17: #2 predicted fragment length is 41 bps INFO @ Sun, 21 Jun 2020 17:24:17: #2 alternative fragment length(s) may be 3,41 bps INFO @ Sun, 21 Jun 2020 17:24:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX066245/SRX066245.20_model.r WARNING @ Sun, 21 Jun 2020 17:24:17: #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 17:24:17: #2 You may need to consider one of the other alternative d(s): 3,41 WARNING @ Sun, 21 Jun 2020 17:24:17: #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 17:24:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:24:17: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:24:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:24:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX066245/SRX066245.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:24:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX066245/SRX066245.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:24:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX066245/SRX066245.20_summits.bed INFO @ Sun, 21 Jun 2020 17:24:39: Done! pass1 - making usageList (424 chroms): 1 millis pass2 - checking and writing primary data (1295 records, 4 fields): 12 millis CompletedMACS2peakCalling