Job ID = 16439288 SRX = SRX15206469 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:22 4414203 reads; of these: 4414203 (100.00%) were unpaired; of these: 75504 (1.71%) aligned 0 times 1809936 (41.00%) aligned exactly 1 time 2528763 (57.29%) aligned >1 times 98.29% overall alignment rate Time searching: 00:02:23 Overall time: 00:02:23 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] 453532 / 4338699 = 0.1045 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 14:55:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206469/SRX15206469.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206469/SRX15206469.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206469/SRX15206469.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206469/SRX15206469.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 14:55:01: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:55:01: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:55:10: 1000000 INFO @ Tue, 02 Aug 2022 14:55:19: 2000000 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 14:55:28: 3000000 INFO @ Tue, 02 Aug 2022 14:55:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206469/SRX15206469.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206469/SRX15206469.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206469/SRX15206469.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206469/SRX15206469.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 14:55:29: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:55:29: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:55:36: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:55:36: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:55:36: #1 total tags in treatment: 3885167 INFO @ Tue, 02 Aug 2022 14:55:36: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:55:36: #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 14:55:36: #1 tags after filtering in treatment: 3885014 INFO @ Tue, 02 Aug 2022 14:55:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:55:36: #1 finished! INFO @ Tue, 02 Aug 2022 14:55:36: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:55:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:55:37: #2 number of paired peaks: 2596 INFO @ Tue, 02 Aug 2022 14:55:37: start model_add_line... INFO @ Tue, 02 Aug 2022 14:55:37: start X-correlation... INFO @ Tue, 02 Aug 2022 14:55:37: end of X-cor INFO @ Tue, 02 Aug 2022 14:55:37: #2 finished! INFO @ Tue, 02 Aug 2022 14:55:37: #2 predicted fragment length is 78 bps INFO @ Tue, 02 Aug 2022 14:55:37: #2 alternative fragment length(s) may be 78,598 bps INFO @ Tue, 02 Aug 2022 14:55:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206469/SRX15206469.05_model.r WARNING @ Tue, 02 Aug 2022 14:55:37: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:55:37: #2 You may need to consider one of the other alternative d(s): 78,598 WARNING @ Tue, 02 Aug 2022 14:55:37: #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 14:55:37: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:55:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:55:38: 1000000 INFO @ Tue, 02 Aug 2022 14:55:48: 2000000 INFO @ Tue, 02 Aug 2022 14:55:50: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:55:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206469/SRX15206469.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:55:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206469/SRX15206469.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:55:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206469/SRX15206469.05_summits.bed INFO @ Tue, 02 Aug 2022 14:55:56: Done! BedGraph に変換中... pass1 - making usageList (706 chroms): 4 millis 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 pass2 - checking and writing primary data (2350 records, 4 fields): 47 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:55:57: 3000000 INFO @ Tue, 02 Aug 2022 14:55:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206469/SRX15206469.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206469/SRX15206469.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206469/SRX15206469.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206469/SRX15206469.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 14:55:59: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:55:59: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:56:06: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:56:06: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:56:06: #1 total tags in treatment: 3885167 INFO @ Tue, 02 Aug 2022 14:56:06: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:56:06: #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 14:56:06: #1 tags after filtering in treatment: 3885014 INFO @ Tue, 02 Aug 2022 14:56:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:56:06: #1 finished! INFO @ Tue, 02 Aug 2022 14:56:06: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:56:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:56:07: #2 number of paired peaks: 2596 INFO @ Tue, 02 Aug 2022 14:56:07: start model_add_line... INFO @ Tue, 02 Aug 2022 14:56:07: start X-correlation... INFO @ Tue, 02 Aug 2022 14:56:07: end of X-cor INFO @ Tue, 02 Aug 2022 14:56:07: #2 finished! INFO @ Tue, 02 Aug 2022 14:56:07: #2 predicted fragment length is 78 bps INFO @ Tue, 02 Aug 2022 14:56:07: #2 alternative fragment length(s) may be 78,598 bps INFO @ Tue, 02 Aug 2022 14:56:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206469/SRX15206469.10_model.r WARNING @ Tue, 02 Aug 2022 14:56:07: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:56:07: #2 You may need to consider one of the other alternative d(s): 78,598 WARNING @ Tue, 02 Aug 2022 14:56:07: #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 14:56:07: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:56:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:56:08: 1000000 INFO @ Tue, 02 Aug 2022 14:56:16: 2000000 INFO @ Tue, 02 Aug 2022 14:56:20: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:56:24: 3000000 INFO @ Tue, 02 Aug 2022 14:56:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206469/SRX15206469.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:56:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206469/SRX15206469.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:56:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206469/SRX15206469.10_summits.bed INFO @ Tue, 02 Aug 2022 14:56:26: Done! pass1 - making usageList (602 chroms): 3 millis pass2 - checking and writing primary data (1579 records, 4 fields): 62 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:56:31: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:56:31: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:56:31: #1 total tags in treatment: 3885167 INFO @ Tue, 02 Aug 2022 14:56:31: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:56:31: #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 14:56:32: #1 tags after filtering in treatment: 3885014 INFO @ Tue, 02 Aug 2022 14:56:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:56:32: #1 finished! INFO @ Tue, 02 Aug 2022 14:56:32: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:56:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:56:32: #2 number of paired peaks: 2596 INFO @ Tue, 02 Aug 2022 14:56:32: start model_add_line... INFO @ Tue, 02 Aug 2022 14:56:32: start X-correlation... INFO @ Tue, 02 Aug 2022 14:56:32: end of X-cor INFO @ Tue, 02 Aug 2022 14:56:32: #2 finished! INFO @ Tue, 02 Aug 2022 14:56:32: #2 predicted fragment length is 78 bps INFO @ Tue, 02 Aug 2022 14:56:32: #2 alternative fragment length(s) may be 78,598 bps INFO @ Tue, 02 Aug 2022 14:56:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206469/SRX15206469.20_model.r WARNING @ Tue, 02 Aug 2022 14:56:33: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:56:33: #2 You may need to consider one of the other alternative d(s): 78,598 WARNING @ Tue, 02 Aug 2022 14:56:33: #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 14:56:33: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:56:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:56:45: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:56:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206469/SRX15206469.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:56:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206469/SRX15206469.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:56:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206469/SRX15206469.20_summits.bed INFO @ Tue, 02 Aug 2022 14:56:51: Done! pass1 - making usageList (421 chroms): 2 millis pass2 - checking and writing primary data (835 records, 4 fields): 52 millis CompletedMACS2peakCalling