Job ID = 5721288 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 26,173,946 reads read : 26,173,946 reads written : 26,173,946 rm: cannot remove ‘[DSE]RR*’: 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: 00:03:09 26173946 reads; of these: 26173946 (100.00%) were unpaired; of these: 21982604 (83.99%) aligned 0 times 3034815 (11.59%) aligned exactly 1 time 1156527 (4.42%) aligned >1 times 16.01% overall alignment rate Time searching: 00:03:09 Overall time: 00:03:09 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] 1526377 / 4191342 = 0.3642 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 06:35:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7672883/SRX7672883.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7672883/SRX7672883.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7672883/SRX7672883.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7672883/SRX7672883.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 06:35:15: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:35:15: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:35:21: 1000000 INFO @ Thu, 16 Apr 2020 06:35:27: 2000000 INFO @ Thu, 16 Apr 2020 06:35:30: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:35:30: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:35:30: #1 total tags in treatment: 2664965 INFO @ Thu, 16 Apr 2020 06:35:30: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:35:30: #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 06:35:30: #1 tags after filtering in treatment: 2664965 INFO @ Thu, 16 Apr 2020 06:35:30: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:35:30: #1 finished! INFO @ Thu, 16 Apr 2020 06:35:30: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:35:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:35:31: #2 number of paired peaks: 508 WARNING @ Thu, 16 Apr 2020 06:35:31: Fewer paired peaks (508) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 508 pairs to build model! INFO @ Thu, 16 Apr 2020 06:35:31: start model_add_line... INFO @ Thu, 16 Apr 2020 06:35:31: start X-correlation... INFO @ Thu, 16 Apr 2020 06:35:31: end of X-cor INFO @ Thu, 16 Apr 2020 06:35:31: #2 finished! INFO @ Thu, 16 Apr 2020 06:35:31: #2 predicted fragment length is 49 bps INFO @ Thu, 16 Apr 2020 06:35:31: #2 alternative fragment length(s) may be 49 bps INFO @ Thu, 16 Apr 2020 06:35:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7672883/SRX7672883.05_model.r WARNING @ Thu, 16 Apr 2020 06:35:31: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:35:31: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Thu, 16 Apr 2020 06:35:31: #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 06:35:31: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:35:31: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:35:37: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:35:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7672883/SRX7672883.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:35:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7672883/SRX7672883.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:35:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7672883/SRX7672883.05_summits.bed INFO @ Thu, 16 Apr 2020 06:35:40: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1463 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 06:35:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7672883/SRX7672883.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7672883/SRX7672883.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7672883/SRX7672883.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7672883/SRX7672883.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 06:35:44: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:35:44: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:35:50: 1000000 INFO @ Thu, 16 Apr 2020 06:35:56: 2000000 INFO @ Thu, 16 Apr 2020 06:35:59: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:35:59: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:35:59: #1 total tags in treatment: 2664965 INFO @ Thu, 16 Apr 2020 06:35:59: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:35:59: #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 06:35:59: #1 tags after filtering in treatment: 2664965 INFO @ Thu, 16 Apr 2020 06:35:59: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:35:59: #1 finished! INFO @ Thu, 16 Apr 2020 06:35:59: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:35:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:36:00: #2 number of paired peaks: 508 WARNING @ Thu, 16 Apr 2020 06:36:00: Fewer paired peaks (508) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 508 pairs to build model! INFO @ Thu, 16 Apr 2020 06:36:00: start model_add_line... INFO @ Thu, 16 Apr 2020 06:36:00: start X-correlation... INFO @ Thu, 16 Apr 2020 06:36:00: end of X-cor INFO @ Thu, 16 Apr 2020 06:36:00: #2 finished! INFO @ Thu, 16 Apr 2020 06:36:00: #2 predicted fragment length is 49 bps INFO @ Thu, 16 Apr 2020 06:36:00: #2 alternative fragment length(s) may be 49 bps INFO @ Thu, 16 Apr 2020 06:36:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7672883/SRX7672883.10_model.r WARNING @ Thu, 16 Apr 2020 06:36:00: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:36:00: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Thu, 16 Apr 2020 06:36:00: #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 06:36:00: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:36:00: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:36:06: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:36:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7672883/SRX7672883.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:36:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7672883/SRX7672883.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:36:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7672883/SRX7672883.10_summits.bed INFO @ Thu, 16 Apr 2020 06:36:09: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1074 records, 4 fields): 13 millis CompletedMACS2peakCalling 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 06:36:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7672883/SRX7672883.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7672883/SRX7672883.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7672883/SRX7672883.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7672883/SRX7672883.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 06:36:15: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:36:15: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:36:20: 1000000 INFO @ Thu, 16 Apr 2020 06:36:26: 2000000 INFO @ Thu, 16 Apr 2020 06:36:30: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:36:30: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:36:30: #1 total tags in treatment: 2664965 INFO @ Thu, 16 Apr 2020 06:36:30: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:36:30: #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 06:36:30: #1 tags after filtering in treatment: 2664965 INFO @ Thu, 16 Apr 2020 06:36:30: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:36:30: #1 finished! INFO @ Thu, 16 Apr 2020 06:36:30: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:36:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:36:30: #2 number of paired peaks: 508 WARNING @ Thu, 16 Apr 2020 06:36:30: Fewer paired peaks (508) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 508 pairs to build model! INFO @ Thu, 16 Apr 2020 06:36:30: start model_add_line... INFO @ Thu, 16 Apr 2020 06:36:30: start X-correlation... INFO @ Thu, 16 Apr 2020 06:36:30: end of X-cor INFO @ Thu, 16 Apr 2020 06:36:30: #2 finished! INFO @ Thu, 16 Apr 2020 06:36:30: #2 predicted fragment length is 49 bps INFO @ Thu, 16 Apr 2020 06:36:30: #2 alternative fragment length(s) may be 49 bps INFO @ Thu, 16 Apr 2020 06:36:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7672883/SRX7672883.20_model.r WARNING @ Thu, 16 Apr 2020 06:36:30: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:36:30: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Thu, 16 Apr 2020 06:36:30: #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 06:36:30: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:36:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:36:36: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:36:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7672883/SRX7672883.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:36:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7672883/SRX7672883.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:36:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7672883/SRX7672883.20_summits.bed INFO @ Thu, 16 Apr 2020 06:36:39: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (544 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。