Job ID = 5720468 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,492,442 reads read : 21,492,442 reads written : 21,492,442 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289691.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: 00:06:25 21492442 reads; of these: 21492442 (100.00%) were unpaired; of these: 1641597 (7.64%) aligned 0 times 15729884 (73.19%) aligned exactly 1 time 4120961 (19.17%) aligned >1 times 92.36% overall alignment rate Time searching: 00:06:25 Overall time: 00:06:25 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_rmdupse_core] 7192327 / 19850845 = 0.3623 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 00:39:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592414/SRX2592414.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592414/SRX2592414.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592414/SRX2592414.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592414/SRX2592414.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 00:39:42: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:39:42: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:39:47: 1000000 INFO @ Thu, 16 Apr 2020 00:39:53: 2000000 INFO @ Thu, 16 Apr 2020 00:39:58: 3000000 INFO @ Thu, 16 Apr 2020 00:40:04: 4000000 INFO @ Thu, 16 Apr 2020 00:40:09: 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 00:40:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592414/SRX2592414.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592414/SRX2592414.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592414/SRX2592414.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592414/SRX2592414.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 00:40:12: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:40:12: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:40:15: 6000000 INFO @ Thu, 16 Apr 2020 00:40:18: 1000000 INFO @ Thu, 16 Apr 2020 00:40:21: 7000000 INFO @ Thu, 16 Apr 2020 00:40:24: 2000000 INFO @ Thu, 16 Apr 2020 00:40:27: 8000000 INFO @ Thu, 16 Apr 2020 00:40:30: 3000000 INFO @ Thu, 16 Apr 2020 00:40:33: 9000000 INFO @ Thu, 16 Apr 2020 00:40:36: 4000000 INFO @ Thu, 16 Apr 2020 00:40:39: 10000000 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 00:40:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592414/SRX2592414.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592414/SRX2592414.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592414/SRX2592414.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592414/SRX2592414.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 00:40:42: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:40:42: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:40:42: 5000000 INFO @ Thu, 16 Apr 2020 00:40:45: 11000000 INFO @ Thu, 16 Apr 2020 00:40:48: 6000000 INFO @ Thu, 16 Apr 2020 00:40:48: 1000000 INFO @ Thu, 16 Apr 2020 00:40:51: 12000000 INFO @ Thu, 16 Apr 2020 00:40:54: 7000000 INFO @ Thu, 16 Apr 2020 00:40:55: 2000000 INFO @ Thu, 16 Apr 2020 00:40:56: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:40:56: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:40:56: #1 total tags in treatment: 12658518 INFO @ Thu, 16 Apr 2020 00:40:56: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:40:56: #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 00:40:56: #1 tags after filtering in treatment: 12658518 INFO @ Thu, 16 Apr 2020 00:40:56: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:40:56: #1 finished! INFO @ Thu, 16 Apr 2020 00:40:56: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:40:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:40:57: #2 number of paired peaks: 565 WARNING @ Thu, 16 Apr 2020 00:40:57: Fewer paired peaks (565) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 565 pairs to build model! INFO @ Thu, 16 Apr 2020 00:40:57: start model_add_line... INFO @ Thu, 16 Apr 2020 00:40:57: start X-correlation... INFO @ Thu, 16 Apr 2020 00:40:57: end of X-cor INFO @ Thu, 16 Apr 2020 00:40:57: #2 finished! INFO @ Thu, 16 Apr 2020 00:40:57: #2 predicted fragment length is 201 bps INFO @ Thu, 16 Apr 2020 00:40:57: #2 alternative fragment length(s) may be 201 bps INFO @ Thu, 16 Apr 2020 00:40:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592414/SRX2592414.05_model.r INFO @ Thu, 16 Apr 2020 00:40:57: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:40:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:41:01: 8000000 INFO @ Thu, 16 Apr 2020 00:41:02: 3000000 INFO @ Thu, 16 Apr 2020 00:41:07: 9000000 INFO @ Thu, 16 Apr 2020 00:41:08: 4000000 INFO @ Thu, 16 Apr 2020 00:41:13: 10000000 INFO @ Thu, 16 Apr 2020 00:41:14: 5000000 INFO @ Thu, 16 Apr 2020 00:41:19: 11000000 INFO @ Thu, 16 Apr 2020 00:41:20: 6000000 INFO @ Thu, 16 Apr 2020 00:41:25: 12000000 INFO @ Thu, 16 Apr 2020 00:41:26: 7000000 INFO @ Thu, 16 Apr 2020 00:41:28: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:41:28: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:41:28: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:41:28: #1 total tags in treatment: 12658518 INFO @ Thu, 16 Apr 2020 00:41:28: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:41:28: #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 00:41:29: #1 tags after filtering in treatment: 12658518 INFO @ Thu, 16 Apr 2020 00:41:29: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:41:29: #1 finished! INFO @ Thu, 16 Apr 2020 00:41:29: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:41:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:41:30: #2 number of paired peaks: 565 WARNING @ Thu, 16 Apr 2020 00:41:30: Fewer paired peaks (565) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 565 pairs to build model! INFO @ Thu, 16 Apr 2020 00:41:30: start model_add_line... INFO @ Thu, 16 Apr 2020 00:41:30: start X-correlation... INFO @ Thu, 16 Apr 2020 00:41:30: end of X-cor INFO @ Thu, 16 Apr 2020 00:41:30: #2 finished! INFO @ Thu, 16 Apr 2020 00:41:30: #2 predicted fragment length is 201 bps INFO @ Thu, 16 Apr 2020 00:41:30: #2 alternative fragment length(s) may be 201 bps INFO @ Thu, 16 Apr 2020 00:41:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592414/SRX2592414.10_model.r INFO @ Thu, 16 Apr 2020 00:41:30: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:41:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:41:32: 8000000 INFO @ Thu, 16 Apr 2020 00:41:38: 9000000 INFO @ Thu, 16 Apr 2020 00:41:43: 10000000 INFO @ Thu, 16 Apr 2020 00:41:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592414/SRX2592414.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:41:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592414/SRX2592414.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:41:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592414/SRX2592414.05_summits.bed INFO @ Thu, 16 Apr 2020 00:41:44: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (16270 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:41:49: 11000000 INFO @ Thu, 16 Apr 2020 00:41:54: 12000000 INFO @ Thu, 16 Apr 2020 00:41:58: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:41:58: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:41:58: #1 total tags in treatment: 12658518 INFO @ Thu, 16 Apr 2020 00:41:58: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:41:58: #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 00:41:58: #1 tags after filtering in treatment: 12658518 INFO @ Thu, 16 Apr 2020 00:41:58: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:41:58: #1 finished! INFO @ Thu, 16 Apr 2020 00:41:58: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:41:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:41:59: #2 number of paired peaks: 565 WARNING @ Thu, 16 Apr 2020 00:41:59: Fewer paired peaks (565) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 565 pairs to build model! INFO @ Thu, 16 Apr 2020 00:41:59: start model_add_line... INFO @ Thu, 16 Apr 2020 00:41:59: start X-correlation... INFO @ Thu, 16 Apr 2020 00:41:59: end of X-cor INFO @ Thu, 16 Apr 2020 00:41:59: #2 finished! INFO @ Thu, 16 Apr 2020 00:41:59: #2 predicted fragment length is 201 bps INFO @ Thu, 16 Apr 2020 00:41:59: #2 alternative fragment length(s) may be 201 bps INFO @ Thu, 16 Apr 2020 00:41:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592414/SRX2592414.20_model.r INFO @ Thu, 16 Apr 2020 00:41:59: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:41:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:42:01: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:42:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592414/SRX2592414.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:42:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592414/SRX2592414.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:42:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592414/SRX2592414.10_summits.bed INFO @ Thu, 16 Apr 2020 00:42:16: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (11860 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:42:33: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:42:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592414/SRX2592414.20_peaks.xls BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 00:42:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592414/SRX2592414.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:42:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592414/SRX2592414.20_summits.bed INFO @ Thu, 16 Apr 2020 00:42:50: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7406 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。