Job ID = 16439150 SRX = SRX15206532 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: 00:08:20 13967764 reads; of these: 13967764 (100.00%) were unpaired; of these: 1560764 (11.17%) aligned 0 times 10742458 (76.91%) aligned exactly 1 time 1664542 (11.92%) aligned >1 times 88.83% overall alignment rate Time searching: 00:08:21 Overall time: 00:08:21 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_sort_core] merging from 12 files... [bam_rmdupse_core] 9680634 / 12407000 = 0.7803 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:50:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206532/SRX15206532.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206532/SRX15206532.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206532/SRX15206532.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206532/SRX15206532.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 @ Tue, 02 Aug 2022 14:50:29: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:50:29: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:50:38: 1000000 INFO @ Tue, 02 Aug 2022 14:50:48: 2000000 INFO @ Tue, 02 Aug 2022 14:50:55: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 14:50:55: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 14:50:55: #1 total tags in treatment: 2726366 INFO @ Tue, 02 Aug 2022 14:50:55: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:50:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:50:55: #1 tags after filtering in treatment: 2726096 INFO @ Tue, 02 Aug 2022 14:50:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:50:55: #1 finished! INFO @ Tue, 02 Aug 2022 14:50:55: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:50:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:50:55: #2 number of paired peaks: 849 WARNING @ Tue, 02 Aug 2022 14:50:55: Fewer paired peaks (849) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 849 pairs to build model! INFO @ Tue, 02 Aug 2022 14:50:55: start model_add_line... INFO @ Tue, 02 Aug 2022 14:50:55: start X-correlation... INFO @ Tue, 02 Aug 2022 14:50:55: end of X-cor INFO @ Tue, 02 Aug 2022 14:50:55: #2 finished! INFO @ Tue, 02 Aug 2022 14:50:55: #2 predicted fragment length is 194 bps INFO @ Tue, 02 Aug 2022 14:50:55: #2 alternative fragment length(s) may be 194 bps INFO @ Tue, 02 Aug 2022 14:50:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206532/SRX15206532.05_model.r WARNING @ Tue, 02 Aug 2022 14:50:55: #2 Since the d (194) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:50:55: #2 You may need to consider one of the other alternative d(s): 194 WARNING @ Tue, 02 Aug 2022 14:50:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:50:55: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:50:55: #3 Pre-compute pvalue-qvalue table... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:50:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206532/SRX15206532.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206532/SRX15206532.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206532/SRX15206532.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206532/SRX15206532.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 @ Tue, 02 Aug 2022 14:50:59: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:50:59: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:51:02: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:51:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206532/SRX15206532.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:51:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206532/SRX15206532.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:51:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206532/SRX15206532.05_summits.bed INFO @ Tue, 02 Aug 2022 14:51:05: Done! pass1 - making usageList (272 chroms): 1 millis pass2 - checking and writing primary data (868 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:51:07: 1000000 INFO @ Tue, 02 Aug 2022 14:51:14: 2000000 INFO @ Tue, 02 Aug 2022 14:51:21: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 14:51:21: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 14:51:21: #1 total tags in treatment: 2726366 INFO @ Tue, 02 Aug 2022 14:51:21: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:51:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:51:21: #1 tags after filtering in treatment: 2726096 INFO @ Tue, 02 Aug 2022 14:51:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:51:21: #1 finished! INFO @ Tue, 02 Aug 2022 14:51:21: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:51:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:51:21: #2 number of paired peaks: 849 WARNING @ Tue, 02 Aug 2022 14:51:21: Fewer paired peaks (849) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 849 pairs to build model! INFO @ Tue, 02 Aug 2022 14:51:21: start model_add_line... INFO @ Tue, 02 Aug 2022 14:51:21: start X-correlation... INFO @ Tue, 02 Aug 2022 14:51:21: end of X-cor INFO @ Tue, 02 Aug 2022 14:51:21: #2 finished! INFO @ Tue, 02 Aug 2022 14:51:21: #2 predicted fragment length is 194 bps INFO @ Tue, 02 Aug 2022 14:51:21: #2 alternative fragment length(s) may be 194 bps INFO @ Tue, 02 Aug 2022 14:51:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206532/SRX15206532.10_model.r WARNING @ Tue, 02 Aug 2022 14:51:21: #2 Since the d (194) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:51:21: #2 You may need to consider one of the other alternative d(s): 194 WARNING @ Tue, 02 Aug 2022 14:51:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:51:21: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:51:21: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:51:28: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:51:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206532/SRX15206532.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206532/SRX15206532.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206532/SRX15206532.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206532/SRX15206532.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 @ Tue, 02 Aug 2022 14:51:28: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:51:28: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:51:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206532/SRX15206532.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:51:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206532/SRX15206532.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:51:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206532/SRX15206532.10_summits.bed INFO @ Tue, 02 Aug 2022 14:51:31: Done! pass1 - making usageList (159 chroms): 1 millis pass2 - checking and writing primary data (389 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:51:37: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:51:46: 2000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:51:53: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 14:51:53: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 14:51:53: #1 total tags in treatment: 2726366 INFO @ Tue, 02 Aug 2022 14:51:53: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:51:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:51:53: #1 tags after filtering in treatment: 2726096 INFO @ Tue, 02 Aug 2022 14:51:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:51:53: #1 finished! INFO @ Tue, 02 Aug 2022 14:51:53: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:51:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:51:53: #2 number of paired peaks: 849 WARNING @ Tue, 02 Aug 2022 14:51:53: Fewer paired peaks (849) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 849 pairs to build model! INFO @ Tue, 02 Aug 2022 14:51:53: start model_add_line... INFO @ Tue, 02 Aug 2022 14:51:53: start X-correlation... INFO @ Tue, 02 Aug 2022 14:51:53: end of X-cor INFO @ Tue, 02 Aug 2022 14:51:53: #2 finished! INFO @ Tue, 02 Aug 2022 14:51:53: #2 predicted fragment length is 194 bps INFO @ Tue, 02 Aug 2022 14:51:53: #2 alternative fragment length(s) may be 194 bps INFO @ Tue, 02 Aug 2022 14:51:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206532/SRX15206532.20_model.r WARNING @ Tue, 02 Aug 2022 14:51:53: #2 Since the d (194) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:51:53: #2 You may need to consider one of the other alternative d(s): 194 WARNING @ Tue, 02 Aug 2022 14:51:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:51:53: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:51:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:52:00: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:52:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206532/SRX15206532.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:52:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206532/SRX15206532.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:52:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206532/SRX15206532.20_summits.bed INFO @ Tue, 02 Aug 2022 14:52:03: Done! pass1 - making usageList (84 chroms): 1 millis pass2 - checking and writing primary data (185 records, 4 fields): 15 millis CompletedMACS2peakCalling