Job ID = 6455644 SRX = SRX287952 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:09:51 prefetch.2.10.7: 1) Downloading 'SRR870141'... 2020-06-21T10:09:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:14:03 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:14:03 prefetch.2.10.7: 1) 'SRR870141' was downloaded successfully Read 21425213 spots for SRR870141/SRR870141.sra Written 21425213 spots for SRR870141/SRR870141.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: 00:08:52 21425213 reads; of these: 21425213 (100.00%) were unpaired; of these: 5522034 (25.77%) aligned 0 times 5814783 (27.14%) aligned exactly 1 time 10088396 (47.09%) aligned >1 times 74.23% overall alignment rate Time searching: 00:08:52 Overall time: 00:08:52 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] 9158929 / 15903179 = 0.5759 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 19:27:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287952/SRX287952.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287952/SRX287952.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287952/SRX287952.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287952/SRX287952.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 19:27:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:27:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:27:44: 1000000 INFO @ Sun, 21 Jun 2020 19:27:52: 2000000 INFO @ Sun, 21 Jun 2020 19:28:00: 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 @ Sun, 21 Jun 2020 19:28:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287952/SRX287952.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287952/SRX287952.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287952/SRX287952.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287952/SRX287952.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 19:28:06: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:28:06: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:28:09: 4000000 INFO @ Sun, 21 Jun 2020 19:28:15: 1000000 INFO @ Sun, 21 Jun 2020 19:28:18: 5000000 INFO @ Sun, 21 Jun 2020 19:28:24: 2000000 INFO @ Sun, 21 Jun 2020 19:28:29: 6000000 INFO @ Sun, 21 Jun 2020 19:28:33: 3000000 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 19:28:36: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:28:36: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:28:36: #1 total tags in treatment: 6744250 INFO @ Sun, 21 Jun 2020 19:28:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:28:36: #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 19:28:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287952/SRX287952.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287952/SRX287952.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287952/SRX287952.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287952/SRX287952.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 19:28:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:28:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:28:37: #1 tags after filtering in treatment: 6744248 INFO @ Sun, 21 Jun 2020 19:28:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:28:37: #1 finished! INFO @ Sun, 21 Jun 2020 19:28:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:28:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:28:37: #2 number of paired peaks: 1538 INFO @ Sun, 21 Jun 2020 19:28:37: start model_add_line... INFO @ Sun, 21 Jun 2020 19:28:37: start X-correlation... INFO @ Sun, 21 Jun 2020 19:28:37: end of X-cor INFO @ Sun, 21 Jun 2020 19:28:37: #2 finished! INFO @ Sun, 21 Jun 2020 19:28:37: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 19:28:37: #2 alternative fragment length(s) may be 4,50 bps INFO @ Sun, 21 Jun 2020 19:28:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287952/SRX287952.05_model.r WARNING @ Sun, 21 Jun 2020 19:28:37: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:28:37: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Sun, 21 Jun 2020 19:28:37: #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 19:28:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:28:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:28:42: 4000000 INFO @ Sun, 21 Jun 2020 19:28:45: 1000000 INFO @ Sun, 21 Jun 2020 19:28:51: 5000000 INFO @ Sun, 21 Jun 2020 19:28:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:28:54: 2000000 INFO @ Sun, 21 Jun 2020 19:29:00: 6000000 INFO @ Sun, 21 Jun 2020 19:29:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287952/SRX287952.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:29:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287952/SRX287952.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:29:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287952/SRX287952.05_summits.bed INFO @ Sun, 21 Jun 2020 19:29:01: Done! pass1 - making usageList (800 chroms): 2 millis pass2 - checking and writing primary data (3257 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:29:04: 3000000 INFO @ Sun, 21 Jun 2020 19:29:07: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:29:07: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:29:07: #1 total tags in treatment: 6744250 INFO @ Sun, 21 Jun 2020 19:29:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:29:07: #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 19:29:08: #1 tags after filtering in treatment: 6744248 INFO @ Sun, 21 Jun 2020 19:29:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:29:08: #1 finished! INFO @ Sun, 21 Jun 2020 19:29:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:29:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:29:08: #2 number of paired peaks: 1538 INFO @ Sun, 21 Jun 2020 19:29:08: start model_add_line... INFO @ Sun, 21 Jun 2020 19:29:08: start X-correlation... INFO @ Sun, 21 Jun 2020 19:29:08: end of X-cor INFO @ Sun, 21 Jun 2020 19:29:08: #2 finished! INFO @ Sun, 21 Jun 2020 19:29:08: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 19:29:08: #2 alternative fragment length(s) may be 4,50 bps INFO @ Sun, 21 Jun 2020 19:29:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287952/SRX287952.10_model.r WARNING @ Sun, 21 Jun 2020 19:29:08: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:29:08: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Sun, 21 Jun 2020 19:29:08: #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 19:29:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:29:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:29:12: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:29:20: 5000000 INFO @ Sun, 21 Jun 2020 19:29:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:29:29: 6000000 INFO @ Sun, 21 Jun 2020 19:29:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287952/SRX287952.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:29:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287952/SRX287952.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:29:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287952/SRX287952.10_summits.bed INFO @ Sun, 21 Jun 2020 19:29:31: Done! pass1 - making usageList (587 chroms): 2 millis pass2 - checking and writing primary data (2182 records, 4 fields): 19 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:29:35: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:29:35: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:29:35: #1 total tags in treatment: 6744250 INFO @ Sun, 21 Jun 2020 19:29:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:29:35: #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 19:29:35: #1 tags after filtering in treatment: 6744248 INFO @ Sun, 21 Jun 2020 19:29:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:29:35: #1 finished! INFO @ Sun, 21 Jun 2020 19:29:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:29:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:29:36: #2 number of paired peaks: 1538 INFO @ Sun, 21 Jun 2020 19:29:36: start model_add_line... INFO @ Sun, 21 Jun 2020 19:29:36: start X-correlation... INFO @ Sun, 21 Jun 2020 19:29:36: end of X-cor INFO @ Sun, 21 Jun 2020 19:29:36: #2 finished! INFO @ Sun, 21 Jun 2020 19:29:36: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 19:29:36: #2 alternative fragment length(s) may be 4,50 bps INFO @ Sun, 21 Jun 2020 19:29:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287952/SRX287952.20_model.r WARNING @ Sun, 21 Jun 2020 19:29:36: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:29:36: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Sun, 21 Jun 2020 19:29:36: #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 19:29:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:29:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:29:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:29:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287952/SRX287952.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:29:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287952/SRX287952.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:29:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287952/SRX287952.20_summits.bed INFO @ Sun, 21 Jun 2020 19:29:58: Done! pass1 - making usageList (459 chroms): 1 millis pass2 - checking and writing primary data (1334 records, 4 fields): 15 millis CompletedMACS2peakCalling