Job ID = 5720555 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,538,420 reads read : 22,538,420 reads written : 22,538,420 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289700.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: 00:08:33 22538420 reads; of these: 22538420 (100.00%) were unpaired; of these: 1554027 (6.90%) aligned 0 times 15431014 (68.47%) aligned exactly 1 time 5553379 (24.64%) aligned >1 times 93.10% overall alignment rate Time searching: 00:08:33 Overall time: 00:08:33 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] 4588601 / 20984393 = 0.2187 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 00:45:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592423/SRX2592423.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592423/SRX2592423.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592423/SRX2592423.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592423/SRX2592423.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 00:45:33: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:45:33: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:45:39: 1000000 INFO @ Thu, 16 Apr 2020 00:45:45: 2000000 INFO @ Thu, 16 Apr 2020 00:45:50: 3000000 INFO @ Thu, 16 Apr 2020 00:45:56: 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 00:46:02: 5000000 INFO @ Thu, 16 Apr 2020 00:46:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592423/SRX2592423.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592423/SRX2592423.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592423/SRX2592423.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592423/SRX2592423.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 00:46:03: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:46:03: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:46:09: 6000000 INFO @ Thu, 16 Apr 2020 00:46:11: 1000000 INFO @ Thu, 16 Apr 2020 00:46:16: 7000000 INFO @ Thu, 16 Apr 2020 00:46:19: 2000000 INFO @ Thu, 16 Apr 2020 00:46:23: 8000000 INFO @ Thu, 16 Apr 2020 00:46:27: 3000000 INFO @ Thu, 16 Apr 2020 00:46:31: 9000000 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 00:46:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592423/SRX2592423.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592423/SRX2592423.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592423/SRX2592423.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592423/SRX2592423.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 00:46:35: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:46:35: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:46:35: 4000000 INFO @ Thu, 16 Apr 2020 00:46:40: 10000000 INFO @ Thu, 16 Apr 2020 00:46:43: 1000000 INFO @ Thu, 16 Apr 2020 00:46:44: 5000000 INFO @ Thu, 16 Apr 2020 00:46:49: 11000000 INFO @ Thu, 16 Apr 2020 00:46:52: 2000000 INFO @ Thu, 16 Apr 2020 00:46:53: 6000000 INFO @ Thu, 16 Apr 2020 00:46:58: 12000000 INFO @ Thu, 16 Apr 2020 00:47:00: 3000000 INFO @ Thu, 16 Apr 2020 00:47:03: 7000000 INFO @ Thu, 16 Apr 2020 00:47:08: 13000000 INFO @ Thu, 16 Apr 2020 00:47:08: 4000000 INFO @ Thu, 16 Apr 2020 00:47:12: 8000000 INFO @ Thu, 16 Apr 2020 00:47:17: 5000000 INFO @ Thu, 16 Apr 2020 00:47:17: 14000000 INFO @ Thu, 16 Apr 2020 00:47:22: 9000000 INFO @ Thu, 16 Apr 2020 00:47:25: 6000000 INFO @ Thu, 16 Apr 2020 00:47:26: 15000000 INFO @ Thu, 16 Apr 2020 00:47:32: 10000000 INFO @ Thu, 16 Apr 2020 00:47:34: 7000000 INFO @ Thu, 16 Apr 2020 00:47:35: 16000000 INFO @ Thu, 16 Apr 2020 00:47:38: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:47:38: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:47:38: #1 total tags in treatment: 16395792 INFO @ Thu, 16 Apr 2020 00:47:38: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:47:38: #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 00:47:39: #1 tags after filtering in treatment: 16395792 INFO @ Thu, 16 Apr 2020 00:47:39: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:47:39: #1 finished! INFO @ Thu, 16 Apr 2020 00:47:39: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:47:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:47:40: #2 number of paired peaks: 106 WARNING @ Thu, 16 Apr 2020 00:47:40: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Thu, 16 Apr 2020 00:47:40: start model_add_line... INFO @ Thu, 16 Apr 2020 00:47:40: start X-correlation... INFO @ Thu, 16 Apr 2020 00:47:40: end of X-cor INFO @ Thu, 16 Apr 2020 00:47:40: #2 finished! INFO @ Thu, 16 Apr 2020 00:47:40: #2 predicted fragment length is 55 bps INFO @ Thu, 16 Apr 2020 00:47:40: #2 alternative fragment length(s) may be 55 bps INFO @ Thu, 16 Apr 2020 00:47:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592423/SRX2592423.05_model.r WARNING @ Thu, 16 Apr 2020 00:47:40: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:47:40: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Thu, 16 Apr 2020 00:47:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 00:47:40: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:47:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:47:42: 11000000 INFO @ Thu, 16 Apr 2020 00:47:45: 8000000 INFO @ Thu, 16 Apr 2020 00:47:50: 12000000 INFO @ Thu, 16 Apr 2020 00:47:55: 9000000 INFO @ Thu, 16 Apr 2020 00:47:58: 13000000 INFO @ Thu, 16 Apr 2020 00:48:05: 10000000 INFO @ Thu, 16 Apr 2020 00:48:06: 14000000 INFO @ Thu, 16 Apr 2020 00:48:13: 11000000 INFO @ Thu, 16 Apr 2020 00:48:15: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:48:16: 15000000 INFO @ Thu, 16 Apr 2020 00:48:23: 12000000 INFO @ Thu, 16 Apr 2020 00:48:25: 16000000 INFO @ Thu, 16 Apr 2020 00:48:30: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:48:30: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:48:30: #1 total tags in treatment: 16395792 INFO @ Thu, 16 Apr 2020 00:48:30: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:48:30: #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 00:48:30: #1 tags after filtering in treatment: 16395792 INFO @ Thu, 16 Apr 2020 00:48:30: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:48:30: #1 finished! INFO @ Thu, 16 Apr 2020 00:48:30: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:48:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:48:32: #2 number of paired peaks: 106 WARNING @ Thu, 16 Apr 2020 00:48:32: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Thu, 16 Apr 2020 00:48:32: start model_add_line... INFO @ Thu, 16 Apr 2020 00:48:32: start X-correlation... INFO @ Thu, 16 Apr 2020 00:48:32: end of X-cor INFO @ Thu, 16 Apr 2020 00:48:32: #2 finished! INFO @ Thu, 16 Apr 2020 00:48:32: #2 predicted fragment length is 55 bps INFO @ Thu, 16 Apr 2020 00:48:32: #2 alternative fragment length(s) may be 55 bps INFO @ Thu, 16 Apr 2020 00:48:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592423/SRX2592423.10_model.r WARNING @ Thu, 16 Apr 2020 00:48:32: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:48:32: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Thu, 16 Apr 2020 00:48:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 00:48:32: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:48:32: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:48:32: 13000000 INFO @ Thu, 16 Apr 2020 00:48:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592423/SRX2592423.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:48:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592423/SRX2592423.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:48:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592423/SRX2592423.05_summits.bed INFO @ Thu, 16 Apr 2020 00:48:33: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (11910 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:48:42: 14000000 INFO @ Thu, 16 Apr 2020 00:48:49: 15000000 INFO @ Thu, 16 Apr 2020 00:48:57: 16000000 INFO @ Thu, 16 Apr 2020 00:49:00: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:49:00: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:49:00: #1 total tags in treatment: 16395792 INFO @ Thu, 16 Apr 2020 00:49:00: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:49:00: #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 00:49:00: #1 tags after filtering in treatment: 16395792 INFO @ Thu, 16 Apr 2020 00:49:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:49:00: #1 finished! INFO @ Thu, 16 Apr 2020 00:49:00: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:49:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:49:01: #2 number of paired peaks: 106 WARNING @ Thu, 16 Apr 2020 00:49:01: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Thu, 16 Apr 2020 00:49:01: start model_add_line... INFO @ Thu, 16 Apr 2020 00:49:01: start X-correlation... INFO @ Thu, 16 Apr 2020 00:49:01: end of X-cor INFO @ Thu, 16 Apr 2020 00:49:01: #2 finished! INFO @ Thu, 16 Apr 2020 00:49:01: #2 predicted fragment length is 55 bps INFO @ Thu, 16 Apr 2020 00:49:01: #2 alternative fragment length(s) may be 55 bps INFO @ Thu, 16 Apr 2020 00:49:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592423/SRX2592423.20_model.r WARNING @ Thu, 16 Apr 2020 00:49:01: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:49:01: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Thu, 16 Apr 2020 00:49:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 00:49:01: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:49:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:49:06: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:49:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592423/SRX2592423.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:49:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592423/SRX2592423.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:49:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592423/SRX2592423.10_summits.bed INFO @ Thu, 16 Apr 2020 00:49:23: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (6249 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:49:35: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:49:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592423/SRX2592423.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:49:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592423/SRX2592423.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:49:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592423/SRX2592423.20_summits.bed INFO @ Thu, 16 Apr 2020 00:49:50: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (773 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。