Job ID = 6455023 SRX = SRX2638367 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:01:10 prefetch.2.10.7: 1) Downloading 'SRR5341693'... 2020-06-21T10:01:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:04:25 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:04:25 prefetch.2.10.7: 1) 'SRR5341693' was downloaded successfully Read 26111222 spots for SRR5341693/SRR5341693.sra Written 26111222 spots for SRR5341693/SRR5341693.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: 00:12:02 26111222 reads; of these: 26111222 (100.00%) were unpaired; of these: 2541670 (9.73%) aligned 0 times 6418109 (24.58%) aligned exactly 1 time 17151443 (65.69%) aligned >1 times 90.27% overall alignment rate Time searching: 00:12:02 Overall time: 00:12:02 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] 17700052 / 23569552 = 0.7510 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 19:22:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2638367/SRX2638367.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2638367/SRX2638367.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2638367/SRX2638367.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2638367/SRX2638367.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 19:22:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:22:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:22:35: 1000000 INFO @ Sun, 21 Jun 2020 19:22:41: 2000000 INFO @ Sun, 21 Jun 2020 19:22:47: 3000000 INFO @ Sun, 21 Jun 2020 19:22:53: 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 19:23:00: 5000000 INFO @ Sun, 21 Jun 2020 19:23:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2638367/SRX2638367.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2638367/SRX2638367.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2638367/SRX2638367.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2638367/SRX2638367.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 19:23:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:23:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:23:05: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:23:05: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:23:05: #1 total tags in treatment: 5869500 INFO @ Sun, 21 Jun 2020 19:23:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:23:05: #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 19:23:06: #1 tags after filtering in treatment: 5869364 INFO @ Sun, 21 Jun 2020 19:23:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:23:06: #1 finished! INFO @ Sun, 21 Jun 2020 19:23:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:23:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:23:06: #2 number of paired peaks: 3532 INFO @ Sun, 21 Jun 2020 19:23:06: start model_add_line... INFO @ Sun, 21 Jun 2020 19:23:06: start X-correlation... INFO @ Sun, 21 Jun 2020 19:23:06: end of X-cor INFO @ Sun, 21 Jun 2020 19:23:06: #2 finished! INFO @ Sun, 21 Jun 2020 19:23:06: #2 predicted fragment length is 62 bps INFO @ Sun, 21 Jun 2020 19:23:06: #2 alternative fragment length(s) may be 3,62 bps INFO @ Sun, 21 Jun 2020 19:23:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2638367/SRX2638367.05_model.r WARNING @ Sun, 21 Jun 2020 19:23:06: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:23:06: #2 You may need to consider one of the other alternative d(s): 3,62 WARNING @ Sun, 21 Jun 2020 19:23:06: #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 19:23:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:23:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:23:07: 1000000 INFO @ Sun, 21 Jun 2020 19:23:13: 2000000 INFO @ Sun, 21 Jun 2020 19:23:19: 3000000 INFO @ Sun, 21 Jun 2020 19:23:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:23:25: 4000000 INFO @ Sun, 21 Jun 2020 19:23:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2638367/SRX2638367.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:23:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2638367/SRX2638367.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:23:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2638367/SRX2638367.05_summits.bed INFO @ Sun, 21 Jun 2020 19:23:25: Done! pass1 - making usageList (746 chroms): 2 millis pass2 - checking and writing primary data (5091 records, 4 fields): 26 millis CompletedMACS2peakCalling 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 19:23:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2638367/SRX2638367.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2638367/SRX2638367.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2638367/SRX2638367.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2638367/SRX2638367.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 19:23:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:23:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:23:31: 5000000 INFO @ Sun, 21 Jun 2020 19:23:36: 1000000 INFO @ Sun, 21 Jun 2020 19:23:37: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:23:37: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:23:37: #1 total tags in treatment: 5869500 INFO @ Sun, 21 Jun 2020 19:23:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:23:37: #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 19:23:37: #1 tags after filtering in treatment: 5869364 INFO @ Sun, 21 Jun 2020 19:23:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:23:37: #1 finished! INFO @ Sun, 21 Jun 2020 19:23:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:23:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:23:38: #2 number of paired peaks: 3532 INFO @ Sun, 21 Jun 2020 19:23:38: start model_add_line... INFO @ Sun, 21 Jun 2020 19:23:38: start X-correlation... INFO @ Sun, 21 Jun 2020 19:23:38: end of X-cor INFO @ Sun, 21 Jun 2020 19:23:38: #2 finished! INFO @ Sun, 21 Jun 2020 19:23:38: #2 predicted fragment length is 62 bps INFO @ Sun, 21 Jun 2020 19:23:38: #2 alternative fragment length(s) may be 3,62 bps INFO @ Sun, 21 Jun 2020 19:23:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2638367/SRX2638367.10_model.r WARNING @ Sun, 21 Jun 2020 19:23:38: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:23:38: #2 You may need to consider one of the other alternative d(s): 3,62 WARNING @ Sun, 21 Jun 2020 19:23:38: #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 19:23:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:23:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:23:42: 2000000 INFO @ Sun, 21 Jun 2020 19:23:48: 3000000 INFO @ Sun, 21 Jun 2020 19:23:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:23:55: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:23:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2638367/SRX2638367.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:23:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2638367/SRX2638367.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:23:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2638367/SRX2638367.10_summits.bed INFO @ Sun, 21 Jun 2020 19:23:57: Done! pass1 - making usageList (647 chroms): 1 millis pass2 - checking and writing primary data (2634 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:24:01: 5000000 INFO @ Sun, 21 Jun 2020 19:24:06: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 19:24:06: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 19:24:06: #1 total tags in treatment: 5869500 INFO @ Sun, 21 Jun 2020 19:24:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:24:06: #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 19:24:07: #1 tags after filtering in treatment: 5869364 INFO @ Sun, 21 Jun 2020 19:24:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:24:07: #1 finished! INFO @ Sun, 21 Jun 2020 19:24:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:24:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:24:07: #2 number of paired peaks: 3532 INFO @ Sun, 21 Jun 2020 19:24:07: start model_add_line... INFO @ Sun, 21 Jun 2020 19:24:07: start X-correlation... INFO @ Sun, 21 Jun 2020 19:24:07: end of X-cor INFO @ Sun, 21 Jun 2020 19:24:07: #2 finished! INFO @ Sun, 21 Jun 2020 19:24:07: #2 predicted fragment length is 62 bps INFO @ Sun, 21 Jun 2020 19:24:07: #2 alternative fragment length(s) may be 3,62 bps INFO @ Sun, 21 Jun 2020 19:24:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2638367/SRX2638367.20_model.r WARNING @ Sun, 21 Jun 2020 19:24:07: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:24:07: #2 You may need to consider one of the other alternative d(s): 3,62 WARNING @ Sun, 21 Jun 2020 19:24:07: #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 19:24:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:24:07: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:24:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:24:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2638367/SRX2638367.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:24:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2638367/SRX2638367.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:24:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2638367/SRX2638367.20_summits.bed INFO @ Sun, 21 Jun 2020 19:24:26: Done! pass1 - making usageList (546 chroms): 1 millis pass2 - checking and writing primary data (1675 records, 4 fields): 16 millis CompletedMACS2peakCalling