Job ID = 6509231 SRX = SRX750080 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T15:31:06 prefetch.2.10.7: 1) Downloading 'SRR1638772'... 2020-06-26T15:31:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:40:25 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:40:25 prefetch.2.10.7: 1) 'SRR1638772' was downloaded successfully Read 51111551 spots for SRR1638772/SRR1638772.sra Written 51111551 spots for SRR1638772/SRR1638772.sra 2020-06-26T15:44:13 prefetch.2.10.7: 1) Downloading 'SRR1638773'... 2020-06-26T15:44:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:55:48 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:55:48 prefetch.2.10.7: 1) 'SRR1638773' was downloaded successfully Read 50056757 spots for SRR1638773/SRR1638773.sra Written 50056757 spots for SRR1638773/SRR1638773.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: 01:08:12 101168308 reads; of these: 101168308 (100.00%) were unpaired; of these: 15509881 (15.33%) aligned 0 times 58131565 (57.46%) aligned exactly 1 time 27526862 (27.21%) aligned >1 times 84.67% overall alignment rate Time searching: 01:08:12 Overall time: 01:08:13 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 64 files... [bam_rmdupse_core] 80763013 / 85658427 = 0.9428 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 @ Sat, 27 Jun 2020 02:35:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX750080/SRX750080.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX750080/SRX750080.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX750080/SRX750080.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX750080/SRX750080.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 @ Sat, 27 Jun 2020 02:35:20: #1 read tag files... INFO @ Sat, 27 Jun 2020 02:35:20: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 02:35:27: 1000000 INFO @ Sat, 27 Jun 2020 02:35:35: 2000000 INFO @ Sat, 27 Jun 2020 02:35:42: 3000000 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 @ Sat, 27 Jun 2020 02:35:49: 4000000 INFO @ Sat, 27 Jun 2020 02:35:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX750080/SRX750080.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX750080/SRX750080.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX750080/SRX750080.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX750080/SRX750080.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 @ Sat, 27 Jun 2020 02:35:49: #1 read tag files... INFO @ Sat, 27 Jun 2020 02:35:49: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 02:35:56: #1 tag size is determined as 141 bps INFO @ Sat, 27 Jun 2020 02:35:56: #1 tag size = 141 INFO @ Sat, 27 Jun 2020 02:35:56: #1 total tags in treatment: 4895414 INFO @ Sat, 27 Jun 2020 02:35:56: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 02:35:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 02:35:56: #1 tags after filtering in treatment: 4895353 INFO @ Sat, 27 Jun 2020 02:35:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 02:35:56: #1 finished! INFO @ Sat, 27 Jun 2020 02:35:56: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 02:35:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 02:35:56: 1000000 INFO @ Sat, 27 Jun 2020 02:35:57: #2 number of paired peaks: 7023 INFO @ Sat, 27 Jun 2020 02:35:57: start model_add_line... INFO @ Sat, 27 Jun 2020 02:35:57: start X-correlation... INFO @ Sat, 27 Jun 2020 02:35:57: end of X-cor INFO @ Sat, 27 Jun 2020 02:35:57: #2 finished! INFO @ Sat, 27 Jun 2020 02:35:57: #2 predicted fragment length is 157 bps INFO @ Sat, 27 Jun 2020 02:35:57: #2 alternative fragment length(s) may be 157 bps INFO @ Sat, 27 Jun 2020 02:35:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX750080/SRX750080.05_model.r WARNING @ Sat, 27 Jun 2020 02:35:57: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 02:35:57: #2 You may need to consider one of the other alternative d(s): 157 WARNING @ Sat, 27 Jun 2020 02:35:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 02:35:57: #3 Call peaks... INFO @ Sat, 27 Jun 2020 02:35:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 02:36:04: 2000000 INFO @ Sat, 27 Jun 2020 02:36:11: 3000000 INFO @ Sat, 27 Jun 2020 02:36:12: #3 Call peaks for each chromosome... 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 @ Sat, 27 Jun 2020 02:36:18: 4000000 INFO @ Sat, 27 Jun 2020 02:36:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX750080/SRX750080.05_peaks.xls INFO @ Sat, 27 Jun 2020 02:36:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX750080/SRX750080.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 02:36:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX750080/SRX750080.05_summits.bed INFO @ Sat, 27 Jun 2020 02:36:19: Done! pass1 - making usageList (856 chroms): 2 millis pass2 - checking and writing primary data (5568 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 02:36:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX750080/SRX750080.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX750080/SRX750080.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX750080/SRX750080.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX750080/SRX750080.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 @ Sat, 27 Jun 2020 02:36:19: #1 read tag files... INFO @ Sat, 27 Jun 2020 02:36:19: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 02:36:25: #1 tag size is determined as 141 bps INFO @ Sat, 27 Jun 2020 02:36:25: #1 tag size = 141 INFO @ Sat, 27 Jun 2020 02:36:25: #1 total tags in treatment: 4895414 INFO @ Sat, 27 Jun 2020 02:36:25: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 02:36:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 02:36:25: #1 tags after filtering in treatment: 4895353 INFO @ Sat, 27 Jun 2020 02:36:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 02:36:25: #1 finished! INFO @ Sat, 27 Jun 2020 02:36:25: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 02:36:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 02:36:26: #2 number of paired peaks: 7023 INFO @ Sat, 27 Jun 2020 02:36:26: start model_add_line... INFO @ Sat, 27 Jun 2020 02:36:26: start X-correlation... INFO @ Sat, 27 Jun 2020 02:36:26: end of X-cor INFO @ Sat, 27 Jun 2020 02:36:26: #2 finished! INFO @ Sat, 27 Jun 2020 02:36:26: #2 predicted fragment length is 157 bps INFO @ Sat, 27 Jun 2020 02:36:26: #2 alternative fragment length(s) may be 157 bps INFO @ Sat, 27 Jun 2020 02:36:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX750080/SRX750080.10_model.r WARNING @ Sat, 27 Jun 2020 02:36:26: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 02:36:26: #2 You may need to consider one of the other alternative d(s): 157 WARNING @ Sat, 27 Jun 2020 02:36:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 02:36:26: #3 Call peaks... INFO @ Sat, 27 Jun 2020 02:36:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 02:36:28: 1000000 INFO @ Sat, 27 Jun 2020 02:36:37: 2000000 INFO @ Sat, 27 Jun 2020 02:36:42: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 02:36:45: 3000000 INFO @ Sat, 27 Jun 2020 02:36:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX750080/SRX750080.10_peaks.xls INFO @ Sat, 27 Jun 2020 02:36:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX750080/SRX750080.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 02:36:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX750080/SRX750080.10_summits.bed INFO @ Sat, 27 Jun 2020 02:36:48: Done! pass1 - making usageList (697 chroms): 2 millis pass2 - checking and writing primary data (3085 records, 4 fields): 21 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 02:36:54: 4000000 BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 02:37:02: #1 tag size is determined as 141 bps INFO @ Sat, 27 Jun 2020 02:37:02: #1 tag size = 141 INFO @ Sat, 27 Jun 2020 02:37:02: #1 total tags in treatment: 4895414 INFO @ Sat, 27 Jun 2020 02:37:02: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 02:37:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 02:37:02: #1 tags after filtering in treatment: 4895353 INFO @ Sat, 27 Jun 2020 02:37:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 02:37:02: #1 finished! INFO @ Sat, 27 Jun 2020 02:37:02: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 02:37:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 02:37:03: #2 number of paired peaks: 7023 INFO @ Sat, 27 Jun 2020 02:37:03: start model_add_line... INFO @ Sat, 27 Jun 2020 02:37:03: start X-correlation... INFO @ Sat, 27 Jun 2020 02:37:03: end of X-cor INFO @ Sat, 27 Jun 2020 02:37:03: #2 finished! INFO @ Sat, 27 Jun 2020 02:37:03: #2 predicted fragment length is 157 bps INFO @ Sat, 27 Jun 2020 02:37:03: #2 alternative fragment length(s) may be 157 bps INFO @ Sat, 27 Jun 2020 02:37:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX750080/SRX750080.20_model.r WARNING @ Sat, 27 Jun 2020 02:37:03: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 02:37:03: #2 You may need to consider one of the other alternative d(s): 157 WARNING @ Sat, 27 Jun 2020 02:37:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 02:37:03: #3 Call peaks... INFO @ Sat, 27 Jun 2020 02:37:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 02:37:18: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 02:37:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX750080/SRX750080.20_peaks.xls INFO @ Sat, 27 Jun 2020 02:37:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX750080/SRX750080.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 02:37:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX750080/SRX750080.20_summits.bed INFO @ Sat, 27 Jun 2020 02:37:25: Done! pass1 - making usageList (534 chroms): 2 millis pass2 - checking and writing primary data (1751 records, 4 fields): 17 millis CompletedMACS2peakCalling