Job ID = 14170638 SRX = SRX5007617 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:01:49 3230009 reads; of these: 3230009 (100.00%) were unpaired; of these: 2761103 (85.48%) aligned 0 times 349024 (10.81%) aligned exactly 1 time 119882 (3.71%) aligned >1 times 14.52% overall alignment rate Time searching: 00:01:49 Overall time: 00:01:49 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 38658 / 468906 = 0.0824 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 07:43:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5007617/SRX5007617.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5007617/SRX5007617.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5007617/SRX5007617.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5007617/SRX5007617.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 @ Sat, 11 Dec 2021 07:43:27: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:43:27: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:43:31: #1 tag size is determined as 151 bps INFO @ Sat, 11 Dec 2021 07:43:31: #1 tag size = 151 INFO @ Sat, 11 Dec 2021 07:43:31: #1 total tags in treatment: 430248 INFO @ Sat, 11 Dec 2021 07:43:31: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:43:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 07:43:31: #1 tags after filtering in treatment: 429881 INFO @ Sat, 11 Dec 2021 07:43:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:43:31: #1 finished! INFO @ Sat, 11 Dec 2021 07:43:31: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:43:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:43:32: #2 number of paired peaks: 933 WARNING @ Sat, 11 Dec 2021 07:43:32: Fewer paired peaks (933) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 933 pairs to build model! INFO @ Sat, 11 Dec 2021 07:43:32: start model_add_line... INFO @ Sat, 11 Dec 2021 07:43:32: start X-correlation... INFO @ Sat, 11 Dec 2021 07:43:32: end of X-cor INFO @ Sat, 11 Dec 2021 07:43:32: #2 finished! INFO @ Sat, 11 Dec 2021 07:43:32: #2 predicted fragment length is 145 bps INFO @ Sat, 11 Dec 2021 07:43:32: #2 alternative fragment length(s) may be 145,586 bps INFO @ Sat, 11 Dec 2021 07:43:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5007617/SRX5007617.05_model.r WARNING @ Sat, 11 Dec 2021 07:43:32: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:43:32: #2 You may need to consider one of the other alternative d(s): 145,586 WARNING @ Sat, 11 Dec 2021 07:43:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 07:43:32: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:43:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:43:33: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:43:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5007617/SRX5007617.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:43:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5007617/SRX5007617.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:43:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5007617/SRX5007617.05_summits.bed INFO @ Sat, 11 Dec 2021 07:43:33: Done! pass1 - making usageList (247 chroms): 1 millis pass2 - checking and writing primary data (326 records, 4 fields): 7 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 07:43:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5007617/SRX5007617.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5007617/SRX5007617.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5007617/SRX5007617.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5007617/SRX5007617.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 @ Sat, 11 Dec 2021 07:43:57: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:43:57: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:44:00: #1 tag size is determined as 151 bps INFO @ Sat, 11 Dec 2021 07:44:00: #1 tag size = 151 INFO @ Sat, 11 Dec 2021 07:44:00: #1 total tags in treatment: 430248 INFO @ Sat, 11 Dec 2021 07:44:00: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:44:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 07:44:01: #1 tags after filtering in treatment: 429881 INFO @ Sat, 11 Dec 2021 07:44:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:44:01: #1 finished! INFO @ Sat, 11 Dec 2021 07:44:01: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:44:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:44:01: #2 number of paired peaks: 933 WARNING @ Sat, 11 Dec 2021 07:44:01: Fewer paired peaks (933) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 933 pairs to build model! INFO @ Sat, 11 Dec 2021 07:44:01: start model_add_line... INFO @ Sat, 11 Dec 2021 07:44:01: start X-correlation... INFO @ Sat, 11 Dec 2021 07:44:01: end of X-cor INFO @ Sat, 11 Dec 2021 07:44:01: #2 finished! INFO @ Sat, 11 Dec 2021 07:44:01: #2 predicted fragment length is 145 bps INFO @ Sat, 11 Dec 2021 07:44:01: #2 alternative fragment length(s) may be 145,586 bps INFO @ Sat, 11 Dec 2021 07:44:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5007617/SRX5007617.10_model.r WARNING @ Sat, 11 Dec 2021 07:44:01: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:44:01: #2 You may need to consider one of the other alternative d(s): 145,586 WARNING @ Sat, 11 Dec 2021 07:44:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 07:44:01: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:44:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:44:02: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:44:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5007617/SRX5007617.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:44:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5007617/SRX5007617.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:44:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5007617/SRX5007617.10_summits.bed INFO @ Sat, 11 Dec 2021 07:44:02: Done! pass1 - making usageList (119 chroms): 1 millis pass2 - checking and writing primary data (132 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 07:44:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5007617/SRX5007617.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5007617/SRX5007617.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5007617/SRX5007617.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5007617/SRX5007617.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 @ Sat, 11 Dec 2021 07:44:27: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:44:27: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:44:31: #1 tag size is determined as 151 bps INFO @ Sat, 11 Dec 2021 07:44:31: #1 tag size = 151 INFO @ Sat, 11 Dec 2021 07:44:31: #1 total tags in treatment: 430248 INFO @ Sat, 11 Dec 2021 07:44:31: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:44:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 07:44:31: #1 tags after filtering in treatment: 429881 INFO @ Sat, 11 Dec 2021 07:44:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:44:31: #1 finished! INFO @ Sat, 11 Dec 2021 07:44:31: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:44:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:44:31: #2 number of paired peaks: 933 WARNING @ Sat, 11 Dec 2021 07:44:31: Fewer paired peaks (933) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 933 pairs to build model! INFO @ Sat, 11 Dec 2021 07:44:31: start model_add_line... INFO @ Sat, 11 Dec 2021 07:44:31: start X-correlation... INFO @ Sat, 11 Dec 2021 07:44:31: end of X-cor INFO @ Sat, 11 Dec 2021 07:44:31: #2 finished! INFO @ Sat, 11 Dec 2021 07:44:31: #2 predicted fragment length is 145 bps INFO @ Sat, 11 Dec 2021 07:44:31: #2 alternative fragment length(s) may be 145,586 bps INFO @ Sat, 11 Dec 2021 07:44:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5007617/SRX5007617.20_model.r WARNING @ Sat, 11 Dec 2021 07:44:31: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:44:31: #2 You may need to consider one of the other alternative d(s): 145,586 WARNING @ Sat, 11 Dec 2021 07:44:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 07:44:31: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:44:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:44:32: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:44:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5007617/SRX5007617.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:44:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5007617/SRX5007617.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:44:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5007617/SRX5007617.20_summits.bed INFO @ Sat, 11 Dec 2021 07:44:33: Done! pass1 - making usageList (28 chroms): 1 millis pass2 - checking and writing primary data (31 records, 4 fields): 8 millis CompletedMACS2peakCalling