Job ID = 5721220 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 12,234,894 reads read : 24,469,788 reads written : 24,469,788 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:47:27 12234894 reads; of these: 12234894 (100.00%) were paired; of these: 1619990 (13.24%) aligned concordantly 0 times 7969543 (65.14%) aligned concordantly exactly 1 time 2645361 (21.62%) aligned concordantly >1 times ---- 1619990 pairs aligned concordantly 0 times; of these: 452709 (27.95%) aligned discordantly 1 time ---- 1167281 pairs aligned 0 times concordantly or discordantly; of these: 2334562 mates make up the pairs; of these: 1369716 (58.67%) aligned 0 times 224893 (9.63%) aligned exactly 1 time 739953 (31.70%) aligned >1 times 94.40% overall alignment rate Time searching: 00:47:27 Overall time: 00:47:27 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1407909 / 11031791 = 0.1276 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 @ Thu, 16 Apr 2020 06:57:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6845078/SRX6845078.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6845078/SRX6845078.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6845078/SRX6845078.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6845078/SRX6845078.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 @ Thu, 16 Apr 2020 06:57:40: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:57:40: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:57:47: 1000000 INFO @ Thu, 16 Apr 2020 06:57:53: 2000000 INFO @ Thu, 16 Apr 2020 06:57:58: 3000000 INFO @ Thu, 16 Apr 2020 06:58:03: 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 @ Thu, 16 Apr 2020 06:58:09: 5000000 INFO @ Thu, 16 Apr 2020 06:58:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6845078/SRX6845078.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6845078/SRX6845078.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6845078/SRX6845078.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6845078/SRX6845078.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 @ Thu, 16 Apr 2020 06:58:11: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:58:11: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:58:15: 6000000 INFO @ Thu, 16 Apr 2020 06:58:16: 1000000 INFO @ Thu, 16 Apr 2020 06:58:20: 7000000 INFO @ Thu, 16 Apr 2020 06:58:22: 2000000 INFO @ Thu, 16 Apr 2020 06:58:26: 8000000 INFO @ Thu, 16 Apr 2020 06:58:28: 3000000 INFO @ Thu, 16 Apr 2020 06:58:32: 9000000 INFO @ Thu, 16 Apr 2020 06:58:34: 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 @ Thu, 16 Apr 2020 06:58:38: 10000000 INFO @ Thu, 16 Apr 2020 06:58:40: 5000000 INFO @ Thu, 16 Apr 2020 06:58:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6845078/SRX6845078.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6845078/SRX6845078.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6845078/SRX6845078.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6845078/SRX6845078.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 @ Thu, 16 Apr 2020 06:58:40: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:58:40: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:58:44: 11000000 INFO @ Thu, 16 Apr 2020 06:58:46: 6000000 INFO @ Thu, 16 Apr 2020 06:58:47: 1000000 INFO @ Thu, 16 Apr 2020 06:58:50: 12000000 INFO @ Thu, 16 Apr 2020 06:58:52: 7000000 INFO @ Thu, 16 Apr 2020 06:58:54: 2000000 INFO @ Thu, 16 Apr 2020 06:58:56: 13000000 INFO @ Thu, 16 Apr 2020 06:58:58: 8000000 INFO @ Thu, 16 Apr 2020 06:59:00: 3000000 INFO @ Thu, 16 Apr 2020 06:59:02: 14000000 INFO @ Thu, 16 Apr 2020 06:59:04: 9000000 INFO @ Thu, 16 Apr 2020 06:59:07: 4000000 INFO @ Thu, 16 Apr 2020 06:59:08: 15000000 INFO @ Thu, 16 Apr 2020 06:59:10: 10000000 INFO @ Thu, 16 Apr 2020 06:59:14: 5000000 INFO @ Thu, 16 Apr 2020 06:59:14: 16000000 INFO @ Thu, 16 Apr 2020 06:59:16: 11000000 INFO @ Thu, 16 Apr 2020 06:59:20: 17000000 INFO @ Thu, 16 Apr 2020 06:59:21: 6000000 INFO @ Thu, 16 Apr 2020 06:59:22: 12000000 INFO @ Thu, 16 Apr 2020 06:59:26: 18000000 INFO @ Thu, 16 Apr 2020 06:59:28: 7000000 INFO @ Thu, 16 Apr 2020 06:59:28: 13000000 INFO @ Thu, 16 Apr 2020 06:59:32: 19000000 INFO @ Thu, 16 Apr 2020 06:59:34: 14000000 INFO @ Thu, 16 Apr 2020 06:59:34: 8000000 INFO @ Thu, 16 Apr 2020 06:59:38: 20000000 INFO @ Thu, 16 Apr 2020 06:59:40: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 06:59:40: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 06:59:40: #1 total tags in treatment: 9267343 INFO @ Thu, 16 Apr 2020 06:59:40: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:59:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 06:59:40: #1 tags after filtering in treatment: 8796596 INFO @ Thu, 16 Apr 2020 06:59:40: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 16 Apr 2020 06:59:40: #1 finished! INFO @ Thu, 16 Apr 2020 06:59:40: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:59:40: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:59:40: 15000000 INFO @ Thu, 16 Apr 2020 06:59:41: #2 number of paired peaks: 1223 INFO @ Thu, 16 Apr 2020 06:59:41: start model_add_line... INFO @ Thu, 16 Apr 2020 06:59:41: start X-correlation... INFO @ Thu, 16 Apr 2020 06:59:41: end of X-cor INFO @ Thu, 16 Apr 2020 06:59:41: #2 finished! INFO @ Thu, 16 Apr 2020 06:59:41: #2 predicted fragment length is 206 bps INFO @ Thu, 16 Apr 2020 06:59:41: #2 alternative fragment length(s) may be 206 bps INFO @ Thu, 16 Apr 2020 06:59:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6845078/SRX6845078.05_model.r INFO @ Thu, 16 Apr 2020 06:59:41: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:59:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:59:41: 9000000 INFO @ Thu, 16 Apr 2020 06:59:46: 16000000 INFO @ Thu, 16 Apr 2020 06:59:48: 10000000 INFO @ Thu, 16 Apr 2020 06:59:52: 17000000 INFO @ Thu, 16 Apr 2020 06:59:55: 11000000 INFO @ Thu, 16 Apr 2020 06:59:58: 18000000 INFO @ Thu, 16 Apr 2020 07:00:01: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 07:00:02: 12000000 INFO @ Thu, 16 Apr 2020 07:00:04: 19000000 INFO @ Thu, 16 Apr 2020 07:00:08: 13000000 INFO @ Thu, 16 Apr 2020 07:00:10: 20000000 INFO @ Thu, 16 Apr 2020 07:00:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6845078/SRX6845078.05_peaks.xls INFO @ Thu, 16 Apr 2020 07:00:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6845078/SRX6845078.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 07:00:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6845078/SRX6845078.05_summits.bed INFO @ Thu, 16 Apr 2020 07:00:10: Done! INFO @ Thu, 16 Apr 2020 07:00:12: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 07:00:12: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 07:00:12: #1 total tags in treatment: 9267343 INFO @ Thu, 16 Apr 2020 07:00:12: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 07:00:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 07:00:12: #1 tags after filtering in treatment: 8796596 INFO @ Thu, 16 Apr 2020 07:00:12: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 16 Apr 2020 07:00:12: #1 finished! INFO @ Thu, 16 Apr 2020 07:00:12: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 07:00:12: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 07:00:13: #2 number of paired peaks: 1223 INFO @ Thu, 16 Apr 2020 07:00:13: start model_add_line... INFO @ Thu, 16 Apr 2020 07:00:13: start X-correlation... INFO @ Thu, 16 Apr 2020 07:00:13: end of X-cor INFO @ Thu, 16 Apr 2020 07:00:13: #2 finished! INFO @ Thu, 16 Apr 2020 07:00:13: #2 predicted fragment length is 206 bps INFO @ Thu, 16 Apr 2020 07:00:13: #2 alternative fragment length(s) may be 206 bps INFO @ Thu, 16 Apr 2020 07:00:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6845078/SRX6845078.10_model.r INFO @ Thu, 16 Apr 2020 07:00:13: #3 Call peaks... INFO @ Thu, 16 Apr 2020 07:00:13: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2716 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 07:00:15: 14000000 INFO @ Thu, 16 Apr 2020 07:00:22: 15000000 INFO @ Thu, 16 Apr 2020 07:00:28: 16000000 INFO @ Thu, 16 Apr 2020 07:00:33: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 07:00:35: 17000000 INFO @ Thu, 16 Apr 2020 07:00:42: 18000000 INFO @ Thu, 16 Apr 2020 07:00:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6845078/SRX6845078.10_peaks.xls INFO @ Thu, 16 Apr 2020 07:00:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6845078/SRX6845078.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 07:00:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6845078/SRX6845078.10_summits.bed INFO @ Thu, 16 Apr 2020 07:00:42: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1431 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 07:00:48: 19000000 INFO @ Thu, 16 Apr 2020 07:00:55: 20000000 INFO @ Thu, 16 Apr 2020 07:00:56: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 07:00:56: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 07:00:56: #1 total tags in treatment: 9267343 INFO @ Thu, 16 Apr 2020 07:00:56: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 07:00:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 07:00:57: #1 tags after filtering in treatment: 8796596 INFO @ Thu, 16 Apr 2020 07:00:57: #1 Redundant rate of treatment: 0.05 INFO @ Thu, 16 Apr 2020 07:00:57: #1 finished! INFO @ Thu, 16 Apr 2020 07:00:57: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 07:00:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 07:00:57: #2 number of paired peaks: 1223 INFO @ Thu, 16 Apr 2020 07:00:57: start model_add_line... INFO @ Thu, 16 Apr 2020 07:00:57: start X-correlation... INFO @ Thu, 16 Apr 2020 07:00:57: end of X-cor INFO @ Thu, 16 Apr 2020 07:00:57: #2 finished! INFO @ Thu, 16 Apr 2020 07:00:57: #2 predicted fragment length is 206 bps INFO @ Thu, 16 Apr 2020 07:00:57: #2 alternative fragment length(s) may be 206 bps INFO @ Thu, 16 Apr 2020 07:00:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6845078/SRX6845078.20_model.r INFO @ Thu, 16 Apr 2020 07:00:57: #3 Call peaks... INFO @ Thu, 16 Apr 2020 07:00:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 07:01:18: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 07:01:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6845078/SRX6845078.20_peaks.xls INFO @ Thu, 16 Apr 2020 07:01:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6845078/SRX6845078.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 07:01:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6845078/SRX6845078.20_summits.bed INFO @ Thu, 16 Apr 2020 07:01:27: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (708 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。