Job ID = 16439283 SRX = SRX15206456 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: 00:02:18 9678551 reads; of these: 9678551 (100.00%) were unpaired; of these: 5353660 (55.31%) aligned 0 times 3222353 (33.29%) aligned exactly 1 time 1102538 (11.39%) aligned >1 times 44.69% overall alignment rate Time searching: 00:02:18 Overall time: 00:02:18 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] 482424 / 4324891 = 0.1115 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 14:53:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206456/SRX15206456.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206456/SRX15206456.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206456/SRX15206456.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206456/SRX15206456.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 14:53:52: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:53:52: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:53:59: 1000000 INFO @ Tue, 02 Aug 2022 14:54:06: 2000000 INFO @ Tue, 02 Aug 2022 14:54:14: 3000000 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 14:54:20: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:54:20: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:54:20: #1 total tags in treatment: 3842467 INFO @ Tue, 02 Aug 2022 14:54:20: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:54:20: #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 14:54:21: #1 tags after filtering in treatment: 3842233 INFO @ Tue, 02 Aug 2022 14:54:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:54:21: #1 finished! INFO @ Tue, 02 Aug 2022 14:54:21: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:54:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:54:21: #2 number of paired peaks: 2503 INFO @ Tue, 02 Aug 2022 14:54:21: start model_add_line... INFO @ Tue, 02 Aug 2022 14:54:21: start X-correlation... INFO @ Tue, 02 Aug 2022 14:54:21: end of X-cor INFO @ Tue, 02 Aug 2022 14:54:21: #2 finished! INFO @ Tue, 02 Aug 2022 14:54:21: #2 predicted fragment length is 139 bps INFO @ Tue, 02 Aug 2022 14:54:21: #2 alternative fragment length(s) may be 139 bps INFO @ Tue, 02 Aug 2022 14:54:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206456/SRX15206456.05_model.r WARNING @ Tue, 02 Aug 2022 14:54:21: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:54:21: #2 You may need to consider one of the other alternative d(s): 139 WARNING @ Tue, 02 Aug 2022 14:54:21: #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 14:54:21: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:54:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:54:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206456/SRX15206456.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206456/SRX15206456.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206456/SRX15206456.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206456/SRX15206456.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 14:54:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:54:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:54:30: 1000000 INFO @ Tue, 02 Aug 2022 14:54:31: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:54:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206456/SRX15206456.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:54:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206456/SRX15206456.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:54:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206456/SRX15206456.05_summits.bed INFO @ Tue, 02 Aug 2022 14:54:36: Done! pass1 - making usageList (502 chroms): 1 millis pass2 - checking and writing primary data (4186 records, 4 fields): 42 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:54:39: 2000000 INFO @ Tue, 02 Aug 2022 14:54:49: 3000000 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 14:54:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX15206456/SRX15206456.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX15206456/SRX15206456.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX15206456/SRX15206456.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX15206456/SRX15206456.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 14:54:52: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:54:52: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:54:57: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:54:57: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:54:57: #1 total tags in treatment: 3842467 INFO @ Tue, 02 Aug 2022 14:54:57: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:54:57: #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 14:54:57: #1 tags after filtering in treatment: 3842233 INFO @ Tue, 02 Aug 2022 14:54:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:54:57: #1 finished! INFO @ Tue, 02 Aug 2022 14:54:57: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:54:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:54:58: #2 number of paired peaks: 2503 INFO @ Tue, 02 Aug 2022 14:54:58: start model_add_line... INFO @ Tue, 02 Aug 2022 14:54:58: start X-correlation... INFO @ Tue, 02 Aug 2022 14:54:58: end of X-cor INFO @ Tue, 02 Aug 2022 14:54:58: #2 finished! INFO @ Tue, 02 Aug 2022 14:54:58: #2 predicted fragment length is 139 bps INFO @ Tue, 02 Aug 2022 14:54:58: #2 alternative fragment length(s) may be 139 bps INFO @ Tue, 02 Aug 2022 14:54:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206456/SRX15206456.10_model.r WARNING @ Tue, 02 Aug 2022 14:54:58: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:54:58: #2 You may need to consider one of the other alternative d(s): 139 WARNING @ Tue, 02 Aug 2022 14:54:58: #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 14:54:58: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:54:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:55:00: 1000000 INFO @ Tue, 02 Aug 2022 14:55:08: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:55:09: 2000000 INFO @ Tue, 02 Aug 2022 14:55:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206456/SRX15206456.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:55:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206456/SRX15206456.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:55:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206456/SRX15206456.10_summits.bed INFO @ Tue, 02 Aug 2022 14:55:12: Done! pass1 - making usageList (430 chroms): 2 millis pass2 - checking and writing primary data (2104 records, 4 fields): 42 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:55:17: 3000000 INFO @ Tue, 02 Aug 2022 14:55:24: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 14:55:24: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 14:55:24: #1 total tags in treatment: 3842467 INFO @ Tue, 02 Aug 2022 14:55:24: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:55:24: #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 14:55:25: #1 tags after filtering in treatment: 3842233 INFO @ Tue, 02 Aug 2022 14:55:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:55:25: #1 finished! INFO @ Tue, 02 Aug 2022 14:55:25: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:55:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:55:25: #2 number of paired peaks: 2503 INFO @ Tue, 02 Aug 2022 14:55:25: start model_add_line... INFO @ Tue, 02 Aug 2022 14:55:25: start X-correlation... INFO @ Tue, 02 Aug 2022 14:55:26: end of X-cor INFO @ Tue, 02 Aug 2022 14:55:26: #2 finished! INFO @ Tue, 02 Aug 2022 14:55:26: #2 predicted fragment length is 139 bps INFO @ Tue, 02 Aug 2022 14:55:26: #2 alternative fragment length(s) may be 139 bps INFO @ Tue, 02 Aug 2022 14:55:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX15206456/SRX15206456.20_model.r WARNING @ Tue, 02 Aug 2022 14:55:26: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:55:26: #2 You may need to consider one of the other alternative d(s): 139 WARNING @ Tue, 02 Aug 2022 14:55:26: #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 14:55:26: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:55:26: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:55:36: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:55:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX15206456/SRX15206456.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:55:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX15206456/SRX15206456.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:55:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX15206456/SRX15206456.20_summits.bed INFO @ Tue, 02 Aug 2022 14:55:40: Done! pass1 - making usageList (253 chroms): 2 millis pass2 - checking and writing primary data (747 records, 4 fields): 107 millis CompletedMACS2peakCalling