Job ID = 6454805 SRX = SRX2592405 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:28:59 prefetch.2.10.7: 1) Downloading 'SRR5289682'... 2020-06-21T09:28:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:33:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:33:06 prefetch.2.10.7: 1) 'SRR5289682' was downloaded successfully Read 23677165 spots for SRR5289682/SRR5289682.sra Written 23677165 spots for SRR5289682/SRR5289682.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: 00:06:21 23677165 reads; of these: 23677165 (100.00%) were unpaired; of these: 3753883 (15.85%) aligned 0 times 14785989 (62.45%) aligned exactly 1 time 5137293 (21.70%) aligned >1 times 84.15% overall alignment rate Time searching: 00:06:21 Overall time: 00:06:21 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 12 files... [bam_rmdupse_core] 6804906 / 19923282 = 0.3416 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 18:45:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592405/SRX2592405.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592405/SRX2592405.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592405/SRX2592405.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592405/SRX2592405.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 18:45:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:45:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:45:52: 1000000 INFO @ Sun, 21 Jun 2020 18:45:58: 2000000 INFO @ Sun, 21 Jun 2020 18:46:04: 3000000 INFO @ Sun, 21 Jun 2020 18:46:11: 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 18:46:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592405/SRX2592405.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592405/SRX2592405.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592405/SRX2592405.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592405/SRX2592405.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 18:46:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:46:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:46:17: 5000000 INFO @ Sun, 21 Jun 2020 18:46:23: 1000000 INFO @ Sun, 21 Jun 2020 18:46:24: 6000000 INFO @ Sun, 21 Jun 2020 18:46:29: 2000000 INFO @ Sun, 21 Jun 2020 18:46:31: 7000000 INFO @ Sun, 21 Jun 2020 18:46:36: 3000000 INFO @ Sun, 21 Jun 2020 18:46:38: 8000000 INFO @ Sun, 21 Jun 2020 18:46:43: 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 18:46:45: 9000000 INFO @ Sun, 21 Jun 2020 18:46:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2592405/SRX2592405.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2592405/SRX2592405.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2592405/SRX2592405.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2592405/SRX2592405.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 18:46:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:46:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:46:50: 5000000 INFO @ Sun, 21 Jun 2020 18:46:52: 10000000 INFO @ Sun, 21 Jun 2020 18:46:54: 1000000 INFO @ Sun, 21 Jun 2020 18:46:58: 6000000 INFO @ Sun, 21 Jun 2020 18:47:00: 11000000 INFO @ Sun, 21 Jun 2020 18:47:01: 2000000 INFO @ Sun, 21 Jun 2020 18:47:06: 7000000 INFO @ Sun, 21 Jun 2020 18:47:08: 12000000 INFO @ Sun, 21 Jun 2020 18:47:09: 3000000 INFO @ Sun, 21 Jun 2020 18:47:13: 8000000 INFO @ Sun, 21 Jun 2020 18:47:15: 13000000 INFO @ Sun, 21 Jun 2020 18:47:16: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:47:16: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:47:16: #1 total tags in treatment: 13118376 INFO @ Sun, 21 Jun 2020 18:47:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:47:16: #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 18:47:17: #1 tags after filtering in treatment: 13118310 INFO @ Sun, 21 Jun 2020 18:47:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:47:17: #1 finished! INFO @ Sun, 21 Jun 2020 18:47:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:47:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:47:17: 4000000 INFO @ Sun, 21 Jun 2020 18:47:18: #2 number of paired peaks: 1113 INFO @ Sun, 21 Jun 2020 18:47:18: start model_add_line... INFO @ Sun, 21 Jun 2020 18:47:18: start X-correlation... INFO @ Sun, 21 Jun 2020 18:47:18: end of X-cor INFO @ Sun, 21 Jun 2020 18:47:18: #2 finished! INFO @ Sun, 21 Jun 2020 18:47:18: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 18:47:18: #2 alternative fragment length(s) may be 3,59,582,588 bps INFO @ Sun, 21 Jun 2020 18:47:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592405/SRX2592405.05_model.r WARNING @ Sun, 21 Jun 2020 18:47:18: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:47:18: #2 You may need to consider one of the other alternative d(s): 3,59,582,588 WARNING @ Sun, 21 Jun 2020 18:47:18: #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 18:47:18: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:47:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:47:21: 9000000 INFO @ Sun, 21 Jun 2020 18:47:25: 5000000 INFO @ Sun, 21 Jun 2020 18:47:28: 10000000 INFO @ Sun, 21 Jun 2020 18:47:33: 6000000 INFO @ Sun, 21 Jun 2020 18:47:36: 11000000 INFO @ Sun, 21 Jun 2020 18:47:41: 7000000 INFO @ Sun, 21 Jun 2020 18:47:44: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:47:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:47:49: 8000000 INFO @ Sun, 21 Jun 2020 18:47:51: 13000000 INFO @ Sun, 21 Jun 2020 18:47:52: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:47:52: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:47:52: #1 total tags in treatment: 13118376 INFO @ Sun, 21 Jun 2020 18:47:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:47:52: #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 18:47:53: #1 tags after filtering in treatment: 13118310 INFO @ Sun, 21 Jun 2020 18:47:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:47:53: #1 finished! INFO @ Sun, 21 Jun 2020 18:47:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:47:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:47:54: #2 number of paired peaks: 1113 INFO @ Sun, 21 Jun 2020 18:47:54: start model_add_line... INFO @ Sun, 21 Jun 2020 18:47:54: start X-correlation... INFO @ Sun, 21 Jun 2020 18:47:54: end of X-cor INFO @ Sun, 21 Jun 2020 18:47:54: #2 finished! INFO @ Sun, 21 Jun 2020 18:47:54: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 18:47:54: #2 alternative fragment length(s) may be 3,59,582,588 bps INFO @ Sun, 21 Jun 2020 18:47:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592405/SRX2592405.10_model.r WARNING @ Sun, 21 Jun 2020 18:47:54: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:47:54: #2 You may need to consider one of the other alternative d(s): 3,59,582,588 WARNING @ Sun, 21 Jun 2020 18:47:54: #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 18:47:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:47:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:47:57: 9000000 INFO @ Sun, 21 Jun 2020 18:48:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592405/SRX2592405.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:48:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592405/SRX2592405.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:48:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592405/SRX2592405.05_summits.bed INFO @ Sun, 21 Jun 2020 18:48:00: Done! pass1 - making usageList (650 chroms): 1 millis pass2 - checking and writing primary data (2834 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:48:04: 10000000 INFO @ Sun, 21 Jun 2020 18:48:12: 11000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:48:19: 12000000 INFO @ Sun, 21 Jun 2020 18:48:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:48:26: 13000000 INFO @ Sun, 21 Jun 2020 18:48:27: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:48:27: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:48:27: #1 total tags in treatment: 13118376 INFO @ Sun, 21 Jun 2020 18:48:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:48:27: #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 18:48:28: #1 tags after filtering in treatment: 13118310 INFO @ Sun, 21 Jun 2020 18:48:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:48:28: #1 finished! INFO @ Sun, 21 Jun 2020 18:48:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:48:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:48:29: #2 number of paired peaks: 1113 INFO @ Sun, 21 Jun 2020 18:48:29: start model_add_line... INFO @ Sun, 21 Jun 2020 18:48:29: start X-correlation... INFO @ Sun, 21 Jun 2020 18:48:29: end of X-cor INFO @ Sun, 21 Jun 2020 18:48:29: #2 finished! INFO @ Sun, 21 Jun 2020 18:48:29: #2 predicted fragment length is 59 bps INFO @ Sun, 21 Jun 2020 18:48:29: #2 alternative fragment length(s) may be 3,59,582,588 bps INFO @ Sun, 21 Jun 2020 18:48:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2592405/SRX2592405.20_model.r WARNING @ Sun, 21 Jun 2020 18:48:29: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:48:29: #2 You may need to consider one of the other alternative d(s): 3,59,582,588 WARNING @ Sun, 21 Jun 2020 18:48:29: #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 18:48:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:48:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:48:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592405/SRX2592405.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:48:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592405/SRX2592405.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:48:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592405/SRX2592405.10_summits.bed INFO @ Sun, 21 Jun 2020 18:48:35: Done! pass1 - making usageList (490 chroms): 1 millis pass2 - checking and writing primary data (1603 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:48:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:49:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2592405/SRX2592405.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:49:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2592405/SRX2592405.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:49:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2592405/SRX2592405.20_summits.bed INFO @ Sun, 21 Jun 2020 18:49:08: Done! pass1 - making usageList (219 chroms): 1 millis pass2 - checking and writing primary data (474 records, 4 fields): 9 millis CompletedMACS2peakCalling