Job ID = 5720726 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,103,892 reads read : 18,103,892 reads written : 18,103,892 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR7253478.sra.cache’: 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: 00:06:10 18103892 reads; of these: 18103892 (100.00%) were unpaired; of these: 593871 (3.28%) aligned 0 times 9761438 (53.92%) aligned exactly 1 time 7748583 (42.80%) aligned >1 times 96.72% overall alignment rate Time searching: 00:06:10 Overall time: 00:06:10 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 8 files... [bam_rmdupse_core] 2424615 / 17510021 = 0.1385 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 01:12:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158198/SRX4158198.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158198/SRX4158198.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158198/SRX4158198.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158198/SRX4158198.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 01:12:19: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:12:19: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:12:24: 1000000 INFO @ Thu, 16 Apr 2020 01:12:29: 2000000 INFO @ Thu, 16 Apr 2020 01:12:35: 3000000 INFO @ Thu, 16 Apr 2020 01:12:40: 4000000 INFO @ Thu, 16 Apr 2020 01:12:45: 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 01:12:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158198/SRX4158198.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158198/SRX4158198.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158198/SRX4158198.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158198/SRX4158198.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 01:12:48: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:12:48: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:12:51: 6000000 INFO @ Thu, 16 Apr 2020 01:12:54: 1000000 INFO @ Thu, 16 Apr 2020 01:12:56: 7000000 INFO @ Thu, 16 Apr 2020 01:12:59: 2000000 INFO @ Thu, 16 Apr 2020 01:13:01: 8000000 INFO @ Thu, 16 Apr 2020 01:13:05: 3000000 INFO @ Thu, 16 Apr 2020 01:13:06: 9000000 INFO @ Thu, 16 Apr 2020 01:13:10: 4000000 INFO @ Thu, 16 Apr 2020 01:13:11: 10000000 INFO @ Thu, 16 Apr 2020 01:13:15: 5000000 INFO @ Thu, 16 Apr 2020 01:13:16: 11000000 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 01:13:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158198/SRX4158198.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158198/SRX4158198.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158198/SRX4158198.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158198/SRX4158198.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 01:13:18: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:13:18: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:13:21: 6000000 INFO @ Thu, 16 Apr 2020 01:13:22: 12000000 INFO @ Thu, 16 Apr 2020 01:13:24: 1000000 INFO @ Thu, 16 Apr 2020 01:13:27: 7000000 INFO @ Thu, 16 Apr 2020 01:13:27: 13000000 INFO @ Thu, 16 Apr 2020 01:13:29: 2000000 INFO @ Thu, 16 Apr 2020 01:13:32: 8000000 INFO @ Thu, 16 Apr 2020 01:13:32: 14000000 INFO @ Thu, 16 Apr 2020 01:13:34: 3000000 INFO @ Thu, 16 Apr 2020 01:13:37: 9000000 INFO @ Thu, 16 Apr 2020 01:13:38: 15000000 INFO @ Thu, 16 Apr 2020 01:13:38: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 01:13:38: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 01:13:38: #1 total tags in treatment: 15085406 INFO @ Thu, 16 Apr 2020 01:13:38: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:13:38: #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 01:13:38: #1 tags after filtering in treatment: 15085406 INFO @ Thu, 16 Apr 2020 01:13:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:13:38: #1 finished! INFO @ Thu, 16 Apr 2020 01:13:38: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:13:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:13:40: #2 number of paired peaks: 2594 INFO @ Thu, 16 Apr 2020 01:13:40: start model_add_line... INFO @ Thu, 16 Apr 2020 01:13:40: start X-correlation... INFO @ Thu, 16 Apr 2020 01:13:40: end of X-cor INFO @ Thu, 16 Apr 2020 01:13:40: #2 finished! INFO @ Thu, 16 Apr 2020 01:13:40: #2 predicted fragment length is 187 bps INFO @ Thu, 16 Apr 2020 01:13:40: #2 alternative fragment length(s) may be 4,187 bps INFO @ Thu, 16 Apr 2020 01:13:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158198/SRX4158198.05_model.r INFO @ Thu, 16 Apr 2020 01:13:40: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:13:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:13:40: 4000000 INFO @ Thu, 16 Apr 2020 01:13:42: 10000000 INFO @ Thu, 16 Apr 2020 01:13:45: 5000000 INFO @ Thu, 16 Apr 2020 01:13:48: 11000000 INFO @ Thu, 16 Apr 2020 01:13:51: 6000000 INFO @ Thu, 16 Apr 2020 01:13:53: 12000000 INFO @ Thu, 16 Apr 2020 01:13:56: 7000000 INFO @ Thu, 16 Apr 2020 01:13:59: 13000000 INFO @ Thu, 16 Apr 2020 01:14:01: 8000000 INFO @ Thu, 16 Apr 2020 01:14:04: 14000000 INFO @ Thu, 16 Apr 2020 01:14:07: 9000000 INFO @ Thu, 16 Apr 2020 01:14:09: 15000000 INFO @ Thu, 16 Apr 2020 01:14:10: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 01:14:10: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 01:14:10: #1 total tags in treatment: 15085406 INFO @ Thu, 16 Apr 2020 01:14:10: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:14:10: #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 01:14:10: #1 tags after filtering in treatment: 15085406 INFO @ Thu, 16 Apr 2020 01:14:10: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:14:10: #1 finished! INFO @ Thu, 16 Apr 2020 01:14:10: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:14:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:14:11: #2 number of paired peaks: 2594 INFO @ Thu, 16 Apr 2020 01:14:11: start model_add_line... INFO @ Thu, 16 Apr 2020 01:14:11: start X-correlation... INFO @ Thu, 16 Apr 2020 01:14:11: end of X-cor INFO @ Thu, 16 Apr 2020 01:14:11: #2 finished! INFO @ Thu, 16 Apr 2020 01:14:11: #2 predicted fragment length is 187 bps INFO @ Thu, 16 Apr 2020 01:14:11: #2 alternative fragment length(s) may be 4,187 bps INFO @ Thu, 16 Apr 2020 01:14:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158198/SRX4158198.10_model.r INFO @ Thu, 16 Apr 2020 01:14:11: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:14:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:14:12: 10000000 INFO @ Thu, 16 Apr 2020 01:14:17: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:14:17: 11000000 INFO @ Thu, 16 Apr 2020 01:14:23: 12000000 INFO @ Thu, 16 Apr 2020 01:14:28: 13000000 INFO @ Thu, 16 Apr 2020 01:14:33: 14000000 INFO @ Thu, 16 Apr 2020 01:14:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158198/SRX4158198.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:14:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158198/SRX4158198.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:14:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158198/SRX4158198.05_summits.bed INFO @ Thu, 16 Apr 2020 01:14:34: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (12245 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:14:39: 15000000 INFO @ Thu, 16 Apr 2020 01:14:39: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 01:14:39: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 01:14:39: #1 total tags in treatment: 15085406 INFO @ Thu, 16 Apr 2020 01:14:39: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:14:39: #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 01:14:40: #1 tags after filtering in treatment: 15085406 INFO @ Thu, 16 Apr 2020 01:14:40: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:14:40: #1 finished! INFO @ Thu, 16 Apr 2020 01:14:40: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:14:40: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:14:41: #2 number of paired peaks: 2594 INFO @ Thu, 16 Apr 2020 01:14:41: start model_add_line... INFO @ Thu, 16 Apr 2020 01:14:41: start X-correlation... INFO @ Thu, 16 Apr 2020 01:14:41: end of X-cor INFO @ Thu, 16 Apr 2020 01:14:41: #2 finished! INFO @ Thu, 16 Apr 2020 01:14:41: #2 predicted fragment length is 187 bps INFO @ Thu, 16 Apr 2020 01:14:41: #2 alternative fragment length(s) may be 4,187 bps INFO @ Thu, 16 Apr 2020 01:14:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158198/SRX4158198.20_model.r INFO @ Thu, 16 Apr 2020 01:14:41: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:14:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:14:51: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:15:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158198/SRX4158198.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:15:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158198/SRX4158198.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:15:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158198/SRX4158198.10_summits.bed INFO @ Thu, 16 Apr 2020 01:15:07: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6809 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:15:19: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:15:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158198/SRX4158198.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:15:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158198/SRX4158198.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:15:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158198/SRX4158198.20_summits.bed INFO @ Thu, 16 Apr 2020 01:15:35: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2617 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。