Job ID = 6509223 SRX = SRX750074 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T15:29:51 prefetch.2.10.7: 1) Downloading 'SRR1638760'... 2020-06-26T15:29:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:32:03 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:32:03 prefetch.2.10.7: 1) 'SRR1638760' was downloaded successfully Read 21475631 spots for SRR1638760/SRR1638760.sra Written 21475631 spots for SRR1638760/SRR1638760.sra 2020-06-26T15:33:22 prefetch.2.10.7: 1) Downloading 'SRR1638761'... 2020-06-26T15:33:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:35:13 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:35:13 prefetch.2.10.7: 1) 'SRR1638761' was downloaded successfully Read 18992466 spots for SRR1638761/SRR1638761.sra Written 18992466 spots for SRR1638761/SRR1638761.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: 00:11:15 40468097 reads; of these: 40468097 (100.00%) were unpaired; of these: 4438501 (10.97%) aligned 0 times 29418357 (72.70%) aligned exactly 1 time 6611239 (16.34%) aligned >1 times 89.03% overall alignment rate Time searching: 00:11:15 Overall time: 00:11:15 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 16 files... [bam_rmdupse_core] 28672807 / 36029596 = 0.7958 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 00:54:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX750074/SRX750074.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX750074/SRX750074.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX750074/SRX750074.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX750074/SRX750074.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 00:54:16: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:54:16: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:54:22: 1000000 INFO @ Sat, 27 Jun 2020 00:54:28: 2000000 INFO @ Sat, 27 Jun 2020 00:54:34: 3000000 INFO @ Sat, 27 Jun 2020 00:54:40: 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 @ Sat, 27 Jun 2020 00:54:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX750074/SRX750074.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX750074/SRX750074.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX750074/SRX750074.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX750074/SRX750074.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 00:54:46: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:54:46: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:54:47: 5000000 INFO @ Sat, 27 Jun 2020 00:54:53: 1000000 INFO @ Sat, 27 Jun 2020 00:54:53: 6000000 INFO @ Sat, 27 Jun 2020 00:54:59: 2000000 INFO @ Sat, 27 Jun 2020 00:55:00: 7000000 INFO @ Sat, 27 Jun 2020 00:55:02: #1 tag size is determined as 67 bps INFO @ Sat, 27 Jun 2020 00:55:02: #1 tag size = 67 INFO @ Sat, 27 Jun 2020 00:55:02: #1 total tags in treatment: 7356789 INFO @ Sat, 27 Jun 2020 00:55:02: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:55:02: #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 00:55:02: #1 tags after filtering in treatment: 7356772 INFO @ Sat, 27 Jun 2020 00:55:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:55:02: #1 finished! INFO @ Sat, 27 Jun 2020 00:55:02: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:55:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:55:03: #2 number of paired peaks: 6092 INFO @ Sat, 27 Jun 2020 00:55:03: start model_add_line... INFO @ Sat, 27 Jun 2020 00:55:03: start X-correlation... INFO @ Sat, 27 Jun 2020 00:55:03: end of X-cor INFO @ Sat, 27 Jun 2020 00:55:03: #2 finished! INFO @ Sat, 27 Jun 2020 00:55:03: #2 predicted fragment length is 141 bps INFO @ Sat, 27 Jun 2020 00:55:03: #2 alternative fragment length(s) may be 141 bps INFO @ Sat, 27 Jun 2020 00:55:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX750074/SRX750074.05_model.r INFO @ Sat, 27 Jun 2020 00:55:03: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:55:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:55:06: 3000000 INFO @ Sat, 27 Jun 2020 00:55:12: 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 @ Sat, 27 Jun 2020 00:55:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX750074/SRX750074.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX750074/SRX750074.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX750074/SRX750074.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX750074/SRX750074.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 00:55:16: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:55:16: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:55:19: 5000000 INFO @ Sat, 27 Jun 2020 00:55:23: 1000000 INFO @ Sat, 27 Jun 2020 00:55:25: 6000000 INFO @ Sat, 27 Jun 2020 00:55:26: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:55:29: 2000000 INFO @ Sat, 27 Jun 2020 00:55:32: 7000000 INFO @ Sat, 27 Jun 2020 00:55:34: #1 tag size is determined as 67 bps INFO @ Sat, 27 Jun 2020 00:55:34: #1 tag size = 67 INFO @ Sat, 27 Jun 2020 00:55:34: #1 total tags in treatment: 7356789 INFO @ Sat, 27 Jun 2020 00:55:34: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:55:34: #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 00:55:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX750074/SRX750074.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:55:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX750074/SRX750074.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:55:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX750074/SRX750074.05_summits.bed INFO @ Sat, 27 Jun 2020 00:55:35: Done! INFO @ Sat, 27 Jun 2020 00:55:35: #1 tags after filtering in treatment: 7356772 INFO @ Sat, 27 Jun 2020 00:55:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:55:35: #1 finished! INFO @ Sat, 27 Jun 2020 00:55:35: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:55:35: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (647 chroms): 2 millis pass2 - checking and writing primary data (6493 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:55:36: 3000000 INFO @ Sat, 27 Jun 2020 00:55:36: #2 number of paired peaks: 6092 INFO @ Sat, 27 Jun 2020 00:55:36: start model_add_line... INFO @ Sat, 27 Jun 2020 00:55:36: start X-correlation... INFO @ Sat, 27 Jun 2020 00:55:36: end of X-cor INFO @ Sat, 27 Jun 2020 00:55:36: #2 finished! INFO @ Sat, 27 Jun 2020 00:55:36: #2 predicted fragment length is 141 bps INFO @ Sat, 27 Jun 2020 00:55:36: #2 alternative fragment length(s) may be 141 bps INFO @ Sat, 27 Jun 2020 00:55:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX750074/SRX750074.10_model.r INFO @ Sat, 27 Jun 2020 00:55:36: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:55:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:55:42: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:55:48: 5000000 INFO @ Sat, 27 Jun 2020 00:55:55: 6000000 INFO @ Sat, 27 Jun 2020 00:55:59: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:56:01: 7000000 INFO @ Sat, 27 Jun 2020 00:56:04: #1 tag size is determined as 67 bps INFO @ Sat, 27 Jun 2020 00:56:04: #1 tag size = 67 INFO @ Sat, 27 Jun 2020 00:56:04: #1 total tags in treatment: 7356789 INFO @ Sat, 27 Jun 2020 00:56:04: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:56:04: #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 00:56:04: #1 tags after filtering in treatment: 7356772 INFO @ Sat, 27 Jun 2020 00:56:04: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:56:04: #1 finished! INFO @ Sat, 27 Jun 2020 00:56:04: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:56:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:56:05: #2 number of paired peaks: 6092 INFO @ Sat, 27 Jun 2020 00:56:05: start model_add_line... INFO @ Sat, 27 Jun 2020 00:56:05: start X-correlation... INFO @ Sat, 27 Jun 2020 00:56:05: end of X-cor INFO @ Sat, 27 Jun 2020 00:56:05: #2 finished! INFO @ Sat, 27 Jun 2020 00:56:05: #2 predicted fragment length is 141 bps INFO @ Sat, 27 Jun 2020 00:56:05: #2 alternative fragment length(s) may be 141 bps INFO @ Sat, 27 Jun 2020 00:56:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX750074/SRX750074.20_model.r INFO @ Sat, 27 Jun 2020 00:56:05: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:56:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:56:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX750074/SRX750074.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:56:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX750074/SRX750074.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:56:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX750074/SRX750074.10_summits.bed INFO @ Sat, 27 Jun 2020 00:56:08: Done! pass1 - making usageList (498 chroms): 1 millis pass2 - checking and writing primary data (4663 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:56:28: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:56:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX750074/SRX750074.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:56:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX750074/SRX750074.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:56:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX750074/SRX750074.20_summits.bed INFO @ Sat, 27 Jun 2020 00:56:37: Done! pass1 - making usageList (365 chroms): 1 millis pass2 - checking and writing primary data (2956 records, 4 fields): 13 millis CompletedMACS2peakCalling