Job ID = 5720572 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,214,502 reads read : 14,214,502 reads written : 14,214,502 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289709.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: 00:04:26 14214502 reads; of these: 14214502 (100.00%) were unpaired; of these: 1068743 (7.52%) aligned 0 times 10348595 (72.80%) aligned exactly 1 time 2797164 (19.68%) aligned >1 times 92.48% overall alignment rate Time searching: 00:04:26 Overall time: 00:04:26 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] 2441947 / 13145759 = 0.1858 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 00:41:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592432/SRX2592432.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592432/SRX2592432.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592432/SRX2592432.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592432/SRX2592432.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 00:41:05: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:41:05: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:41:10: 1000000 INFO @ Thu, 16 Apr 2020 00:41:15: 2000000 INFO @ Thu, 16 Apr 2020 00:41:20: 3000000 INFO @ Thu, 16 Apr 2020 00:41:25: 4000000 INFO @ Thu, 16 Apr 2020 00:41:30: 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 00:41:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592432/SRX2592432.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592432/SRX2592432.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592432/SRX2592432.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592432/SRX2592432.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 00:41:34: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:41:34: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:41:35: 6000000 INFO @ Thu, 16 Apr 2020 00:41:41: 7000000 INFO @ Thu, 16 Apr 2020 00:41:43: 1000000 INFO @ Thu, 16 Apr 2020 00:41:46: 8000000 INFO @ Thu, 16 Apr 2020 00:41:49: 2000000 INFO @ Thu, 16 Apr 2020 00:41:52: 9000000 INFO @ Thu, 16 Apr 2020 00:41:55: 3000000 INFO @ Thu, 16 Apr 2020 00:41:57: 10000000 INFO @ Thu, 16 Apr 2020 00:42:01: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:42:01: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:42:01: #1 total tags in treatment: 10703812 INFO @ Thu, 16 Apr 2020 00:42:01: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:42:01: #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 00:42:01: 4000000 INFO @ Thu, 16 Apr 2020 00:42:01: #1 tags after filtering in treatment: 10703812 INFO @ Thu, 16 Apr 2020 00:42:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:42:01: #1 finished! INFO @ Thu, 16 Apr 2020 00:42:01: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:42:01: #2 looking for paired plus/minus strand peaks... BedGraph に変換中... INFO @ Thu, 16 Apr 2020 00:42:02: #2 number of paired peaks: 118 WARNING @ Thu, 16 Apr 2020 00:42:02: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Thu, 16 Apr 2020 00:42:02: start model_add_line... 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 00:42:02: start X-correlation... INFO @ Thu, 16 Apr 2020 00:42:02: end of X-cor INFO @ Thu, 16 Apr 2020 00:42:02: #2 finished! INFO @ Thu, 16 Apr 2020 00:42:02: #2 predicted fragment length is 185 bps INFO @ Thu, 16 Apr 2020 00:42:02: #2 alternative fragment length(s) may be 75,94,117,185,214,231,246 bps INFO @ Thu, 16 Apr 2020 00:42:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592432/SRX2592432.05_model.r INFO @ Thu, 16 Apr 2020 00:42:02: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:42:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:42:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592432/SRX2592432.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592432/SRX2592432.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592432/SRX2592432.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592432/SRX2592432.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 00:42:04: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:42:04: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:42:07: 5000000 INFO @ Thu, 16 Apr 2020 00:42:10: 1000000 INFO @ Thu, 16 Apr 2020 00:42:14: 6000000 INFO @ Thu, 16 Apr 2020 00:42:15: 2000000 INFO @ Thu, 16 Apr 2020 00:42:20: 7000000 INFO @ Thu, 16 Apr 2020 00:42:21: 3000000 INFO @ Thu, 16 Apr 2020 00:42:25: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:42:26: 8000000 INFO @ Thu, 16 Apr 2020 00:42:26: 4000000 INFO @ Thu, 16 Apr 2020 00:42:32: 5000000 INFO @ Thu, 16 Apr 2020 00:42:32: 9000000 INFO @ Thu, 16 Apr 2020 00:42:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592432/SRX2592432.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:42:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592432/SRX2592432.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:42:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592432/SRX2592432.05_summits.bed INFO @ Thu, 16 Apr 2020 00:42:37: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (13030 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:42:37: 6000000 INFO @ Thu, 16 Apr 2020 00:42:38: 10000000 INFO @ Thu, 16 Apr 2020 00:42:43: 7000000 INFO @ Thu, 16 Apr 2020 00:42:43: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:42:43: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:42:43: #1 total tags in treatment: 10703812 INFO @ Thu, 16 Apr 2020 00:42:43: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:42:43: #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 00:42:43: #1 tags after filtering in treatment: 10703812 INFO @ Thu, 16 Apr 2020 00:42:43: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:42:43: #1 finished! INFO @ Thu, 16 Apr 2020 00:42:43: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:42:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:42:44: #2 number of paired peaks: 118 WARNING @ Thu, 16 Apr 2020 00:42:44: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Thu, 16 Apr 2020 00:42:44: start model_add_line... INFO @ Thu, 16 Apr 2020 00:42:44: start X-correlation... INFO @ Thu, 16 Apr 2020 00:42:44: end of X-cor INFO @ Thu, 16 Apr 2020 00:42:44: #2 finished! INFO @ Thu, 16 Apr 2020 00:42:44: #2 predicted fragment length is 185 bps INFO @ Thu, 16 Apr 2020 00:42:44: #2 alternative fragment length(s) may be 75,94,117,185,214,231,246 bps INFO @ Thu, 16 Apr 2020 00:42:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592432/SRX2592432.10_model.r INFO @ Thu, 16 Apr 2020 00:42:44: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:42:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:42:48: 8000000 INFO @ Thu, 16 Apr 2020 00:42:53: 9000000 INFO @ Thu, 16 Apr 2020 00:42:59: 10000000 INFO @ Thu, 16 Apr 2020 00:43:03: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:43:03: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:43:03: #1 total tags in treatment: 10703812 INFO @ Thu, 16 Apr 2020 00:43:03: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:43:03: #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 00:43:03: #1 tags after filtering in treatment: 10703812 INFO @ Thu, 16 Apr 2020 00:43:03: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:43:03: #1 finished! INFO @ Thu, 16 Apr 2020 00:43:03: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:43:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:43:04: #2 number of paired peaks: 118 WARNING @ Thu, 16 Apr 2020 00:43:04: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Thu, 16 Apr 2020 00:43:04: start model_add_line... INFO @ Thu, 16 Apr 2020 00:43:04: start X-correlation... INFO @ Thu, 16 Apr 2020 00:43:04: end of X-cor INFO @ Thu, 16 Apr 2020 00:43:04: #2 finished! INFO @ Thu, 16 Apr 2020 00:43:04: #2 predicted fragment length is 185 bps INFO @ Thu, 16 Apr 2020 00:43:04: #2 alternative fragment length(s) may be 75,94,117,185,214,231,246 bps INFO @ Thu, 16 Apr 2020 00:43:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592432/SRX2592432.20_model.r INFO @ Thu, 16 Apr 2020 00:43:04: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:43:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:43:07: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:43:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592432/SRX2592432.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:43:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592432/SRX2592432.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:43:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592432/SRX2592432.10_summits.bed INFO @ Thu, 16 Apr 2020 00:43:19: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (8658 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:43:27: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:43:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592432/SRX2592432.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:43:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592432/SRX2592432.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:43:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592432/SRX2592432.20_summits.bed INFO @ Thu, 16 Apr 2020 00:43:39: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4960 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。