Job ID = 5720657 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,831,465 reads read : 5,831,465 reads written : 5,831,465 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289754.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: 00:01:56 5831465 reads; of these: 5831465 (100.00%) were unpaired; of these: 1219038 (20.90%) aligned 0 times 3292740 (56.47%) aligned exactly 1 time 1319687 (22.63%) aligned >1 times 79.10% overall alignment rate Time searching: 00:01:56 Overall time: 00:01:56 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_rmdupse_core] 1615911 / 4612427 = 0.3503 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 00:50:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592477/SRX2592477.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592477/SRX2592477.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592477/SRX2592477.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592477/SRX2592477.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 00:50:47: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:50:47: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:50:53: 1000000 INFO @ Thu, 16 Apr 2020 00:50:59: 2000000 INFO @ Thu, 16 Apr 2020 00:51:05: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:51:05: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:51:05: #1 total tags in treatment: 2996516 INFO @ Thu, 16 Apr 2020 00:51:05: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:51:05: #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 00:51:06: #1 tags after filtering in treatment: 2996516 INFO @ Thu, 16 Apr 2020 00:51:06: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:51:06: #1 finished! INFO @ Thu, 16 Apr 2020 00:51:06: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:51:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:51:06: #2 number of paired peaks: 963 WARNING @ Thu, 16 Apr 2020 00:51:06: Fewer paired peaks (963) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 963 pairs to build model! INFO @ Thu, 16 Apr 2020 00:51:06: start model_add_line... INFO @ Thu, 16 Apr 2020 00:51:06: start X-correlation... INFO @ Thu, 16 Apr 2020 00:51:06: end of X-cor INFO @ Thu, 16 Apr 2020 00:51:06: #2 finished! INFO @ Thu, 16 Apr 2020 00:51:06: #2 predicted fragment length is 57 bps INFO @ Thu, 16 Apr 2020 00:51:06: #2 alternative fragment length(s) may be 57 bps INFO @ Thu, 16 Apr 2020 00:51:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592477/SRX2592477.05_model.r WARNING @ Thu, 16 Apr 2020 00:51:06: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:51:06: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Thu, 16 Apr 2020 00:51:06: #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 00:51:06: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:51:06: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:51:13: #3 Call peaks for each chromosome... 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 00:51:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592477/SRX2592477.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592477/SRX2592477.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592477/SRX2592477.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592477/SRX2592477.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 00:51:16: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:51:16: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:51:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592477/SRX2592477.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:51:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592477/SRX2592477.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:51:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592477/SRX2592477.05_summits.bed INFO @ Thu, 16 Apr 2020 00:51:17: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1349 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:51:23: 1000000 INFO @ Thu, 16 Apr 2020 00:51:29: 2000000 INFO @ Thu, 16 Apr 2020 00:51:35: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:51:35: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:51:35: #1 total tags in treatment: 2996516 INFO @ Thu, 16 Apr 2020 00:51:35: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:51:35: #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 00:51:35: #1 tags after filtering in treatment: 2996516 INFO @ Thu, 16 Apr 2020 00:51:35: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:51:35: #1 finished! INFO @ Thu, 16 Apr 2020 00:51:35: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:51:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:51:35: #2 number of paired peaks: 963 WARNING @ Thu, 16 Apr 2020 00:51:35: Fewer paired peaks (963) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 963 pairs to build model! INFO @ Thu, 16 Apr 2020 00:51:35: start model_add_line... INFO @ Thu, 16 Apr 2020 00:51:35: start X-correlation... INFO @ Thu, 16 Apr 2020 00:51:35: end of X-cor INFO @ Thu, 16 Apr 2020 00:51:35: #2 finished! INFO @ Thu, 16 Apr 2020 00:51:35: #2 predicted fragment length is 57 bps INFO @ Thu, 16 Apr 2020 00:51:35: #2 alternative fragment length(s) may be 57 bps INFO @ Thu, 16 Apr 2020 00:51:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592477/SRX2592477.10_model.r WARNING @ Thu, 16 Apr 2020 00:51:35: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:51:35: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Thu, 16 Apr 2020 00:51:35: #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 00:51:35: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:51:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:51:42: #3 Call peaks for each chromosome... 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 00:51:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592477/SRX2592477.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:51:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592477/SRX2592477.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:51:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592477/SRX2592477.10_summits.bed INFO @ Thu, 16 Apr 2020 00:51:46: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (912 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:51:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592477/SRX2592477.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592477/SRX2592477.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592477/SRX2592477.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592477/SRX2592477.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 00:51:47: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:51:47: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:51:53: 1000000 INFO @ Thu, 16 Apr 2020 00:51:59: 2000000 INFO @ Thu, 16 Apr 2020 00:52:05: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:52:05: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:52:05: #1 total tags in treatment: 2996516 INFO @ Thu, 16 Apr 2020 00:52:05: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:52:05: #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 00:52:05: #1 tags after filtering in treatment: 2996516 INFO @ Thu, 16 Apr 2020 00:52:05: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:52:05: #1 finished! INFO @ Thu, 16 Apr 2020 00:52:05: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:52:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:52:06: #2 number of paired peaks: 963 WARNING @ Thu, 16 Apr 2020 00:52:06: Fewer paired peaks (963) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 963 pairs to build model! INFO @ Thu, 16 Apr 2020 00:52:06: start model_add_line... INFO @ Thu, 16 Apr 2020 00:52:06: start X-correlation... INFO @ Thu, 16 Apr 2020 00:52:06: end of X-cor INFO @ Thu, 16 Apr 2020 00:52:06: #2 finished! INFO @ Thu, 16 Apr 2020 00:52:06: #2 predicted fragment length is 57 bps INFO @ Thu, 16 Apr 2020 00:52:06: #2 alternative fragment length(s) may be 57 bps INFO @ Thu, 16 Apr 2020 00:52:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592477/SRX2592477.20_model.r WARNING @ Thu, 16 Apr 2020 00:52:06: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:52:06: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Thu, 16 Apr 2020 00:52:06: #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 00:52:06: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:52:06: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:52:13: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:52:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592477/SRX2592477.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:52:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592477/SRX2592477.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:52:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592477/SRX2592477.20_summits.bed INFO @ Thu, 16 Apr 2020 00:52:16: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (674 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。