Job ID = 6453632 SRX = SRX1308481 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:33:54 prefetch.2.10.7: 1) Downloading 'SRR2566775'... 2020-06-21T08:33:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:36:16 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:36:17 prefetch.2.10.7: 'SRR2566775' is valid 2020-06-21T08:36:17 prefetch.2.10.7: 1) 'SRR2566775' was downloaded successfully Read 10020489 spots for SRR2566775/SRR2566775.sra Written 10020489 spots for SRR2566775/SRR2566775.sra 2020-06-21T08:36:57 prefetch.2.10.7: 1) Downloading 'SRR2566776'... 2020-06-21T08:36:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:38:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:38:45 prefetch.2.10.7: 'SRR2566776' is valid 2020-06-21T08:38:45 prefetch.2.10.7: 1) 'SRR2566776' was downloaded successfully Read 10028929 spots for SRR2566776/SRR2566776.sra Written 10028929 spots for SRR2566776/SRR2566776.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: 00:05:17 20049418 reads; of these: 20049418 (100.00%) were unpaired; of these: 1335698 (6.66%) aligned 0 times 15126453 (75.45%) aligned exactly 1 time 3587267 (17.89%) aligned >1 times 93.34% overall alignment rate Time searching: 00:05:17 Overall time: 00:05:17 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] 12559724 / 18713720 = 0.6712 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 17:49:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1308481/SRX1308481.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1308481/SRX1308481.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1308481/SRX1308481.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1308481/SRX1308481.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 17:49:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:49:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:49:11: 1000000 INFO @ Sun, 21 Jun 2020 17:49:16: 2000000 INFO @ Sun, 21 Jun 2020 17:49:21: 3000000 INFO @ Sun, 21 Jun 2020 17:49:26: 4000000 INFO @ Sun, 21 Jun 2020 17:49:31: 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 @ Sun, 21 Jun 2020 17:49:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1308481/SRX1308481.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1308481/SRX1308481.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1308481/SRX1308481.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1308481/SRX1308481.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 17:49:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:49:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:49:36: 6000000 INFO @ Sun, 21 Jun 2020 17:49:37: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:49:37: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:49:37: #1 total tags in treatment: 6153996 INFO @ Sun, 21 Jun 2020 17:49:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:49:37: #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 17:49:38: #1 tags after filtering in treatment: 6153981 INFO @ Sun, 21 Jun 2020 17:49:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:49:38: #1 finished! INFO @ Sun, 21 Jun 2020 17:49:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:49:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:49:38: #2 number of paired peaks: 1227 INFO @ Sun, 21 Jun 2020 17:49:38: start model_add_line... INFO @ Sun, 21 Jun 2020 17:49:38: start X-correlation... INFO @ Sun, 21 Jun 2020 17:49:38: end of X-cor INFO @ Sun, 21 Jun 2020 17:49:38: #2 finished! INFO @ Sun, 21 Jun 2020 17:49:38: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 17:49:38: #2 alternative fragment length(s) may be 4,52 bps INFO @ Sun, 21 Jun 2020 17:49:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1308481/SRX1308481.05_model.r WARNING @ Sun, 21 Jun 2020 17:49:38: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:49:38: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Sun, 21 Jun 2020 17:49:38: #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 17:49:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:49:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:49:41: 1000000 INFO @ Sun, 21 Jun 2020 17:49:46: 2000000 INFO @ Sun, 21 Jun 2020 17:49:51: 3000000 INFO @ Sun, 21 Jun 2020 17:49:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:49:56: 4000000 INFO @ Sun, 21 Jun 2020 17:49:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1308481/SRX1308481.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:49:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1308481/SRX1308481.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:49:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1308481/SRX1308481.05_summits.bed INFO @ Sun, 21 Jun 2020 17:49:58: Done! pass1 - making usageList (542 chroms): 1 millis pass2 - checking and writing primary data (2375 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:50:02: 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 @ Sun, 21 Jun 2020 17:50:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1308481/SRX1308481.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1308481/SRX1308481.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1308481/SRX1308481.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1308481/SRX1308481.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 17:50:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:50:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:50:07: 6000000 INFO @ Sun, 21 Jun 2020 17:50:08: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:50:08: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:50:08: #1 total tags in treatment: 6153996 INFO @ Sun, 21 Jun 2020 17:50:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:50:08: #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 17:50:08: #1 tags after filtering in treatment: 6153981 INFO @ Sun, 21 Jun 2020 17:50:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:50:08: #1 finished! INFO @ Sun, 21 Jun 2020 17:50:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:50:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:50:09: #2 number of paired peaks: 1227 INFO @ Sun, 21 Jun 2020 17:50:09: start model_add_line... INFO @ Sun, 21 Jun 2020 17:50:09: start X-correlation... INFO @ Sun, 21 Jun 2020 17:50:09: end of X-cor INFO @ Sun, 21 Jun 2020 17:50:09: #2 finished! INFO @ Sun, 21 Jun 2020 17:50:09: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 17:50:09: #2 alternative fragment length(s) may be 4,52 bps INFO @ Sun, 21 Jun 2020 17:50:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1308481/SRX1308481.10_model.r WARNING @ Sun, 21 Jun 2020 17:50:09: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:50:09: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Sun, 21 Jun 2020 17:50:09: #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 17:50:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:50:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:50:11: 1000000 INFO @ Sun, 21 Jun 2020 17:50:16: 2000000 INFO @ Sun, 21 Jun 2020 17:50:21: 3000000 INFO @ Sun, 21 Jun 2020 17:50:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:50:27: 4000000 INFO @ Sun, 21 Jun 2020 17:50:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1308481/SRX1308481.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:50:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1308481/SRX1308481.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:50:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1308481/SRX1308481.10_summits.bed INFO @ Sun, 21 Jun 2020 17:50:28: Done! pass1 - making usageList (477 chroms): 1 millis pass2 - checking and writing primary data (1873 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:50:32: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:50:37: 6000000 INFO @ Sun, 21 Jun 2020 17:50:38: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:50:38: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:50:38: #1 total tags in treatment: 6153996 INFO @ Sun, 21 Jun 2020 17:50:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:50:38: #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 17:50:39: #1 tags after filtering in treatment: 6153981 INFO @ Sun, 21 Jun 2020 17:50:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:50:39: #1 finished! INFO @ Sun, 21 Jun 2020 17:50:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:50:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:50:39: #2 number of paired peaks: 1227 INFO @ Sun, 21 Jun 2020 17:50:39: start model_add_line... INFO @ Sun, 21 Jun 2020 17:50:39: start X-correlation... INFO @ Sun, 21 Jun 2020 17:50:39: end of X-cor INFO @ Sun, 21 Jun 2020 17:50:39: #2 finished! INFO @ Sun, 21 Jun 2020 17:50:39: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 17:50:39: #2 alternative fragment length(s) may be 4,52 bps INFO @ Sun, 21 Jun 2020 17:50:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1308481/SRX1308481.20_model.r WARNING @ Sun, 21 Jun 2020 17:50:39: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:50:39: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Sun, 21 Jun 2020 17:50:39: #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 17:50:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:50:39: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:50:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:51:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1308481/SRX1308481.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:51:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1308481/SRX1308481.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:51:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1308481/SRX1308481.20_summits.bed INFO @ Sun, 21 Jun 2020 17:51:00: Done! pass1 - making usageList (373 chroms): 1 millis pass2 - checking and writing primary data (918 records, 4 fields): 13 millis CompletedMACS2peakCalling