Job ID = 5720777 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 22,902,416 reads read : 45,804,832 reads written : 45,804,832 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: 01:59:49 22902416 reads; of these: 22902416 (100.00%) were paired; of these: 5561153 (24.28%) aligned concordantly 0 times 6768509 (29.55%) aligned concordantly exactly 1 time 10572754 (46.16%) aligned concordantly >1 times ---- 5561153 pairs aligned concordantly 0 times; of these: 868790 (15.62%) aligned discordantly 1 time ---- 4692363 pairs aligned 0 times concordantly or discordantly; of these: 9384726 mates make up the pairs; of these: 3580265 (38.15%) aligned 0 times 977523 (10.42%) aligned exactly 1 time 4826938 (51.43%) aligned >1 times 92.18% overall alignment rate Time searching: 01:59:49 Overall time: 01:59:49 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 20 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] 2349169 / 18058655 = 0.1301 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 03:59:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246870/SRX5246870.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246870/SRX5246870.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246870/SRX5246870.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246870/SRX5246870.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 03:59:54: #1 read tag files... INFO @ Thu, 16 Apr 2020 03:59:54: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:00:00: 1000000 INFO @ Thu, 16 Apr 2020 04:00:05: 2000000 INFO @ Thu, 16 Apr 2020 04:00:10: 3000000 INFO @ Thu, 16 Apr 2020 04:00:16: 4000000 INFO @ Thu, 16 Apr 2020 04:00:21: 5000000 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 04:00:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246870/SRX5246870.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246870/SRX5246870.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246870/SRX5246870.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246870/SRX5246870.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 04:00:24: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:00:24: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:00:26: 6000000 INFO @ Thu, 16 Apr 2020 04:00:30: 1000000 INFO @ Thu, 16 Apr 2020 04:00:32: 7000000 INFO @ Thu, 16 Apr 2020 04:00:35: 2000000 INFO @ Thu, 16 Apr 2020 04:00:37: 8000000 INFO @ Thu, 16 Apr 2020 04:00:41: 3000000 INFO @ Thu, 16 Apr 2020 04:00:43: 9000000 INFO @ Thu, 16 Apr 2020 04:00:47: 4000000 INFO @ Thu, 16 Apr 2020 04:00:48: 10000000 INFO @ Thu, 16 Apr 2020 04:00:52: 5000000 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 04:00:54: 11000000 INFO @ Thu, 16 Apr 2020 04:00:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5246870/SRX5246870.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5246870/SRX5246870.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5246870/SRX5246870.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5246870/SRX5246870.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 04:00:54: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:00:54: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:00:58: 6000000 INFO @ Thu, 16 Apr 2020 04:00:59: 12000000 INFO @ Thu, 16 Apr 2020 04:01:00: 1000000 INFO @ Thu, 16 Apr 2020 04:01:04: 7000000 INFO @ Thu, 16 Apr 2020 04:01:05: 13000000 INFO @ Thu, 16 Apr 2020 04:01:06: 2000000 INFO @ Thu, 16 Apr 2020 04:01:09: 8000000 INFO @ Thu, 16 Apr 2020 04:01:10: 14000000 INFO @ Thu, 16 Apr 2020 04:01:12: 3000000 INFO @ Thu, 16 Apr 2020 04:01:15: 9000000 INFO @ Thu, 16 Apr 2020 04:01:16: 15000000 INFO @ Thu, 16 Apr 2020 04:01:18: 4000000 INFO @ Thu, 16 Apr 2020 04:01:21: 10000000 INFO @ Thu, 16 Apr 2020 04:01:22: 16000000 INFO @ Thu, 16 Apr 2020 04:01:23: 5000000 INFO @ Thu, 16 Apr 2020 04:01:26: 11000000 INFO @ Thu, 16 Apr 2020 04:01:27: 17000000 INFO @ Thu, 16 Apr 2020 04:01:29: 6000000 INFO @ Thu, 16 Apr 2020 04:01:32: 12000000 INFO @ Thu, 16 Apr 2020 04:01:33: 18000000 INFO @ Thu, 16 Apr 2020 04:01:35: 7000000 INFO @ Thu, 16 Apr 2020 04:01:38: 13000000 INFO @ Thu, 16 Apr 2020 04:01:38: 19000000 INFO @ Thu, 16 Apr 2020 04:01:40: 8000000 INFO @ Thu, 16 Apr 2020 04:01:43: 14000000 INFO @ Thu, 16 Apr 2020 04:01:44: 20000000 INFO @ Thu, 16 Apr 2020 04:01:46: 9000000 INFO @ Thu, 16 Apr 2020 04:01:49: 15000000 INFO @ Thu, 16 Apr 2020 04:01:50: 21000000 INFO @ Thu, 16 Apr 2020 04:01:52: 10000000 INFO @ Thu, 16 Apr 2020 04:01:54: 16000000 INFO @ Thu, 16 Apr 2020 04:01:56: 22000000 INFO @ Thu, 16 Apr 2020 04:01:57: 11000000 INFO @ Thu, 16 Apr 2020 04:02:00: 17000000 INFO @ Thu, 16 Apr 2020 04:02:01: 23000000 INFO @ Thu, 16 Apr 2020 04:02:03: 12000000 INFO @ Thu, 16 Apr 2020 04:02:06: 18000000 INFO @ Thu, 16 Apr 2020 04:02:07: 24000000 INFO @ Thu, 16 Apr 2020 04:02:08: 13000000 INFO @ Thu, 16 Apr 2020 04:02:11: 19000000 INFO @ Thu, 16 Apr 2020 04:02:13: 25000000 INFO @ Thu, 16 Apr 2020 04:02:14: 14000000 INFO @ Thu, 16 Apr 2020 04:02:17: 20000000 INFO @ Thu, 16 Apr 2020 04:02:18: 26000000 INFO @ Thu, 16 Apr 2020 04:02:19: 15000000 INFO @ Thu, 16 Apr 2020 04:02:23: 21000000 INFO @ Thu, 16 Apr 2020 04:02:24: 27000000 INFO @ Thu, 16 Apr 2020 04:02:25: 16000000 INFO @ Thu, 16 Apr 2020 04:02:28: 22000000 INFO @ Thu, 16 Apr 2020 04:02:29: 28000000 INFO @ Thu, 16 Apr 2020 04:02:30: 17000000 INFO @ Thu, 16 Apr 2020 04:02:34: 23000000 INFO @ Thu, 16 Apr 2020 04:02:35: 29000000 INFO @ Thu, 16 Apr 2020 04:02:36: 18000000 INFO @ Thu, 16 Apr 2020 04:02:40: 24000000 INFO @ Thu, 16 Apr 2020 04:02:40: 30000000 INFO @ Thu, 16 Apr 2020 04:02:41: 19000000 INFO @ Thu, 16 Apr 2020 04:02:45: 25000000 INFO @ Thu, 16 Apr 2020 04:02:46: 31000000 INFO @ Thu, 16 Apr 2020 04:02:47: 20000000 INFO @ Thu, 16 Apr 2020 04:02:51: 26000000 INFO @ Thu, 16 Apr 2020 04:02:52: 32000000 INFO @ Thu, 16 Apr 2020 04:02:53: 21000000 INFO @ Thu, 16 Apr 2020 04:02:57: 27000000 INFO @ Thu, 16 Apr 2020 04:02:57: 33000000 INFO @ Thu, 16 Apr 2020 04:02:59: 22000000 INFO @ Thu, 16 Apr 2020 04:03:02: 28000000 INFO @ Thu, 16 Apr 2020 04:03:03: 34000000 INFO @ Thu, 16 Apr 2020 04:03:04: 23000000 INFO @ Thu, 16 Apr 2020 04:03:08: 29000000 INFO @ Thu, 16 Apr 2020 04:03:09: 35000000 INFO @ Thu, 16 Apr 2020 04:03:10: 24000000 INFO @ Thu, 16 Apr 2020 04:03:13: 30000000 INFO @ Thu, 16 Apr 2020 04:03:14: 36000000 INFO @ Thu, 16 Apr 2020 04:03:16: 25000000 INFO @ Thu, 16 Apr 2020 04:03:19: 31000000 INFO @ Thu, 16 Apr 2020 04:03:20: 37000000 INFO @ Thu, 16 Apr 2020 04:03:21: 26000000 INFO @ Thu, 16 Apr 2020 04:03:23: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 04:03:23: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 04:03:23: #1 total tags in treatment: 15085747 INFO @ Thu, 16 Apr 2020 04:03:23: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:03:23: #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 04:03:23: #1 tags after filtering in treatment: 13011844 INFO @ Thu, 16 Apr 2020 04:03:23: #1 Redundant rate of treatment: 0.14 INFO @ Thu, 16 Apr 2020 04:03:23: #1 finished! INFO @ Thu, 16 Apr 2020 04:03:23: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:03:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:03:24: #2 number of paired peaks: 2630 INFO @ Thu, 16 Apr 2020 04:03:24: start model_add_line... INFO @ Thu, 16 Apr 2020 04:03:24: start X-correlation... INFO @ Thu, 16 Apr 2020 04:03:24: end of X-cor INFO @ Thu, 16 Apr 2020 04:03:24: #2 finished! INFO @ Thu, 16 Apr 2020 04:03:24: #2 predicted fragment length is 209 bps INFO @ Thu, 16 Apr 2020 04:03:24: #2 alternative fragment length(s) may be 209 bps INFO @ Thu, 16 Apr 2020 04:03:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246870/SRX5246870.05_model.r INFO @ Thu, 16 Apr 2020 04:03:24: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:03:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:03:25: 32000000 INFO @ Thu, 16 Apr 2020 04:03:27: 27000000 INFO @ Thu, 16 Apr 2020 04:03:30: 33000000 INFO @ Thu, 16 Apr 2020 04:03:32: 28000000 INFO @ Thu, 16 Apr 2020 04:03:36: 34000000 INFO @ Thu, 16 Apr 2020 04:03:38: 29000000 INFO @ Thu, 16 Apr 2020 04:03:42: 35000000 INFO @ Thu, 16 Apr 2020 04:03:43: 30000000 INFO @ Thu, 16 Apr 2020 04:03:48: 36000000 INFO @ Thu, 16 Apr 2020 04:03:49: 31000000 INFO @ Thu, 16 Apr 2020 04:03:53: 37000000 INFO @ Thu, 16 Apr 2020 04:03:55: 32000000 INFO @ Thu, 16 Apr 2020 04:03:56: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 04:03:56: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 04:03:56: #1 total tags in treatment: 15085747 INFO @ Thu, 16 Apr 2020 04:03:56: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:03:56: #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 04:03:56: #1 tags after filtering in treatment: 13011844 INFO @ Thu, 16 Apr 2020 04:03:56: #1 Redundant rate of treatment: 0.14 INFO @ Thu, 16 Apr 2020 04:03:56: #1 finished! INFO @ Thu, 16 Apr 2020 04:03:56: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:03:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:03:57: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:03:57: #2 number of paired peaks: 2630 INFO @ Thu, 16 Apr 2020 04:03:57: start model_add_line... INFO @ Thu, 16 Apr 2020 04:03:58: start X-correlation... INFO @ Thu, 16 Apr 2020 04:03:58: end of X-cor INFO @ Thu, 16 Apr 2020 04:03:58: #2 finished! INFO @ Thu, 16 Apr 2020 04:03:58: #2 predicted fragment length is 209 bps INFO @ Thu, 16 Apr 2020 04:03:58: #2 alternative fragment length(s) may be 209 bps INFO @ Thu, 16 Apr 2020 04:03:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246870/SRX5246870.10_model.r INFO @ Thu, 16 Apr 2020 04:03:58: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:03:58: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:04:00: 33000000 INFO @ Thu, 16 Apr 2020 04:04:06: 34000000 INFO @ Thu, 16 Apr 2020 04:04:11: 35000000 INFO @ Thu, 16 Apr 2020 04:04:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246870/SRX5246870.05_peaks.xls INFO @ Thu, 16 Apr 2020 04:04:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246870/SRX5246870.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:04:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246870/SRX5246870.05_summits.bed INFO @ Thu, 16 Apr 2020 04:04:14: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (14205 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 04:04:17: 36000000 INFO @ Thu, 16 Apr 2020 04:04:22: 37000000 INFO @ Thu, 16 Apr 2020 04:04:25: #1 tag size is determined as 101 bps INFO @ Thu, 16 Apr 2020 04:04:25: #1 tag size = 101 INFO @ Thu, 16 Apr 2020 04:04:25: #1 total tags in treatment: 15085747 INFO @ Thu, 16 Apr 2020 04:04:25: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:04:25: #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 04:04:26: #1 tags after filtering in treatment: 13011844 INFO @ Thu, 16 Apr 2020 04:04:26: #1 Redundant rate of treatment: 0.14 INFO @ Thu, 16 Apr 2020 04:04:26: #1 finished! INFO @ Thu, 16 Apr 2020 04:04:26: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:04:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:04:27: #2 number of paired peaks: 2630 INFO @ Thu, 16 Apr 2020 04:04:27: start model_add_line... INFO @ Thu, 16 Apr 2020 04:04:27: start X-correlation... INFO @ Thu, 16 Apr 2020 04:04:27: end of X-cor INFO @ Thu, 16 Apr 2020 04:04:27: #2 finished! INFO @ Thu, 16 Apr 2020 04:04:27: #2 predicted fragment length is 209 bps INFO @ Thu, 16 Apr 2020 04:04:27: #2 alternative fragment length(s) may be 209 bps INFO @ Thu, 16 Apr 2020 04:04:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5246870/SRX5246870.20_model.r INFO @ Thu, 16 Apr 2020 04:04:27: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:04:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:04:29: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:04:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246870/SRX5246870.10_peaks.xls INFO @ Thu, 16 Apr 2020 04:04:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246870/SRX5246870.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:04:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246870/SRX5246870.10_summits.bed INFO @ Thu, 16 Apr 2020 04:04:46: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (9483 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 04:04:59: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:05:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5246870/SRX5246870.20_peaks.xls INFO @ Thu, 16 Apr 2020 04:05:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5246870/SRX5246870.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:05:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5246870/SRX5246870.20_summits.bed INFO @ Thu, 16 Apr 2020 04:05:15: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5253 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。