Job ID = 10166576 SRX = SRX7723716 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: 00:04:07 20054790 reads; of these: 20054790 (100.00%) were unpaired; of these: 12632555 (62.99%) aligned 0 times 5545022 (27.65%) aligned exactly 1 time 1877213 (9.36%) aligned >1 times 37.01% overall alignment rate Time searching: 00:04:07 Overall time: 00:04:07 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] 2572542 / 7422235 = 0.3466 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, 08 Oct 2020 21:54:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7723716/SRX7723716.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7723716/SRX7723716.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7723716/SRX7723716.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7723716/SRX7723716.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, 08 Oct 2020 21:54:37: #1 read tag files... INFO @ Thu, 08 Oct 2020 21:54:37: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 21:54:44: 1000000 INFO @ Thu, 08 Oct 2020 21:54:50: 2000000 INFO @ Thu, 08 Oct 2020 21:54:56: 3000000 INFO @ Thu, 08 Oct 2020 21:55:03: 4000000 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, 08 Oct 2020 21:55:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7723716/SRX7723716.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7723716/SRX7723716.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7723716/SRX7723716.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7723716/SRX7723716.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, 08 Oct 2020 21:55:06: #1 read tag files... INFO @ Thu, 08 Oct 2020 21:55:06: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 21:55:09: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 21:55:09: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 21:55:09: #1 total tags in treatment: 4849693 INFO @ Thu, 08 Oct 2020 21:55:09: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 21:55:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 21:55:10: #1 tags after filtering in treatment: 4849457 INFO @ Thu, 08 Oct 2020 21:55:10: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 21:55:10: #1 finished! INFO @ Thu, 08 Oct 2020 21:55:10: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 21:55:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 21:55:10: #2 number of paired peaks: 1342 INFO @ Thu, 08 Oct 2020 21:55:10: start model_add_line... INFO @ Thu, 08 Oct 2020 21:55:10: start X-correlation... INFO @ Thu, 08 Oct 2020 21:55:10: end of X-cor INFO @ Thu, 08 Oct 2020 21:55:10: #2 finished! INFO @ Thu, 08 Oct 2020 21:55:10: #2 predicted fragment length is 83 bps INFO @ Thu, 08 Oct 2020 21:55:10: #2 alternative fragment length(s) may be 83 bps INFO @ Thu, 08 Oct 2020 21:55:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723716/SRX7723716.05_model.r WARNING @ Thu, 08 Oct 2020 21:55:10: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 21:55:10: #2 You may need to consider one of the other alternative d(s): 83 WARNING @ Thu, 08 Oct 2020 21:55:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 21:55:10: #3 Call peaks... INFO @ Thu, 08 Oct 2020 21:55:10: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 21:55:13: 1000000 INFO @ Thu, 08 Oct 2020 21:55:20: 2000000 INFO @ Thu, 08 Oct 2020 21:55:21: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 21:55:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723716/SRX7723716.05_peaks.xls INFO @ Thu, 08 Oct 2020 21:55:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723716/SRX7723716.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 21:55:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723716/SRX7723716.05_summits.bed INFO @ Thu, 08 Oct 2020 21:55:26: Done! pass1 - making usageList (625 chroms): 2 millis pass2 - checking and writing primary data (2062 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 21:55:27: 3000000 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, 08 Oct 2020 21:55:34: 4000000 INFO @ Thu, 08 Oct 2020 21:55:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7723716/SRX7723716.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7723716/SRX7723716.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7723716/SRX7723716.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7723716/SRX7723716.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, 08 Oct 2020 21:55:36: #1 read tag files... INFO @ Thu, 08 Oct 2020 21:55:36: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 21:55:40: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 21:55:40: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 21:55:40: #1 total tags in treatment: 4849693 INFO @ Thu, 08 Oct 2020 21:55:40: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 21:55:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 21:55:41: #1 tags after filtering in treatment: 4849457 INFO @ Thu, 08 Oct 2020 21:55:41: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 21:55:41: #1 finished! INFO @ Thu, 08 Oct 2020 21:55:41: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 21:55:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 21:55:41: #2 number of paired peaks: 1342 INFO @ Thu, 08 Oct 2020 21:55:41: start model_add_line... INFO @ Thu, 08 Oct 2020 21:55:41: start X-correlation... INFO @ Thu, 08 Oct 2020 21:55:41: end of X-cor INFO @ Thu, 08 Oct 2020 21:55:41: #2 finished! INFO @ Thu, 08 Oct 2020 21:55:41: #2 predicted fragment length is 83 bps INFO @ Thu, 08 Oct 2020 21:55:41: #2 alternative fragment length(s) may be 83 bps INFO @ Thu, 08 Oct 2020 21:55:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723716/SRX7723716.10_model.r WARNING @ Thu, 08 Oct 2020 21:55:41: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 21:55:41: #2 You may need to consider one of the other alternative d(s): 83 WARNING @ Thu, 08 Oct 2020 21:55:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 21:55:41: #3 Call peaks... INFO @ Thu, 08 Oct 2020 21:55:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 21:55:43: 1000000 INFO @ Thu, 08 Oct 2020 21:55:50: 2000000 INFO @ Thu, 08 Oct 2020 21:55:52: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 21:55:57: 3000000 INFO @ Thu, 08 Oct 2020 21:55:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723716/SRX7723716.10_peaks.xls INFO @ Thu, 08 Oct 2020 21:55:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723716/SRX7723716.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 21:55:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723716/SRX7723716.10_summits.bed INFO @ Thu, 08 Oct 2020 21:55:57: Done! pass1 - making usageList (548 chroms): 1 millis pass2 - checking and writing primary data (1564 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 21:56:04: 4000000 INFO @ Thu, 08 Oct 2020 21:56:10: #1 tag size is determined as 75 bps INFO @ Thu, 08 Oct 2020 21:56:10: #1 tag size = 75 INFO @ Thu, 08 Oct 2020 21:56:10: #1 total tags in treatment: 4849693 INFO @ Thu, 08 Oct 2020 21:56:10: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 21:56:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 21:56:10: #1 tags after filtering in treatment: 4849457 INFO @ Thu, 08 Oct 2020 21:56:10: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 21:56:10: #1 finished! INFO @ Thu, 08 Oct 2020 21:56:10: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 21:56:10: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 21:56:10: #2 number of paired peaks: 1342 INFO @ Thu, 08 Oct 2020 21:56:10: start model_add_line... INFO @ Thu, 08 Oct 2020 21:56:10: start X-correlation... INFO @ Thu, 08 Oct 2020 21:56:10: end of X-cor INFO @ Thu, 08 Oct 2020 21:56:10: #2 finished! INFO @ Thu, 08 Oct 2020 21:56:10: #2 predicted fragment length is 83 bps INFO @ Thu, 08 Oct 2020 21:56:10: #2 alternative fragment length(s) may be 83 bps INFO @ Thu, 08 Oct 2020 21:56:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723716/SRX7723716.20_model.r WARNING @ Thu, 08 Oct 2020 21:56:10: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 21:56:10: #2 You may need to consider one of the other alternative d(s): 83 WARNING @ Thu, 08 Oct 2020 21:56:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 21:56:10: #3 Call peaks... INFO @ Thu, 08 Oct 2020 21:56:10: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 21:56:21: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 21:56:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723716/SRX7723716.20_peaks.xls INFO @ Thu, 08 Oct 2020 21:56:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723716/SRX7723716.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 21:56:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723716/SRX7723716.20_summits.bed INFO @ Thu, 08 Oct 2020 21:56:26: Done! pass1 - making usageList (411 chroms): 1 millis pass2 - checking and writing primary data (870 records, 4 fields): 13 millis CompletedMACS2peakCalling