Job ID = 14172514 SRX = SRX10089756 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: 00:05:32 32307893 reads; of these: 32307893 (100.00%) were unpaired; of these: 24403679 (75.53%) aligned 0 times 6299085 (19.50%) aligned exactly 1 time 1605129 (4.97%) aligned >1 times 24.47% overall alignment rate Time searching: 00:05:32 Overall time: 00:05:32 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] 910559 / 7904214 = 0.1152 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 15:53:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10089756/SRX10089756.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10089756/SRX10089756.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10089756/SRX10089756.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10089756/SRX10089756.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 15:53:27: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:53:27: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:53:33: 1000000 INFO @ Sat, 11 Dec 2021 15:53:39: 2000000 INFO @ Sat, 11 Dec 2021 15:53:44: 3000000 INFO @ Sat, 11 Dec 2021 15:53:50: 4000000 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 15:53:55: 5000000 INFO @ Sat, 11 Dec 2021 15:53:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10089756/SRX10089756.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10089756/SRX10089756.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10089756/SRX10089756.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10089756/SRX10089756.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 15:53:57: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:53:57: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:54:01: 6000000 INFO @ Sat, 11 Dec 2021 15:54:03: 1000000 INFO @ Sat, 11 Dec 2021 15:54:07: #1 tag size is determined as 74 bps INFO @ Sat, 11 Dec 2021 15:54:07: #1 tag size = 74 INFO @ Sat, 11 Dec 2021 15:54:07: #1 total tags in treatment: 6993655 INFO @ Sat, 11 Dec 2021 15:54:07: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:54:07: #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 15:54:08: #1 tags after filtering in treatment: 6993634 INFO @ Sat, 11 Dec 2021 15:54:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:54:08: #1 finished! INFO @ Sat, 11 Dec 2021 15:54:08: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:54:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:54:08: #2 number of paired peaks: 1453 INFO @ Sat, 11 Dec 2021 15:54:08: start model_add_line... INFO @ Sat, 11 Dec 2021 15:54:08: start X-correlation... INFO @ Sat, 11 Dec 2021 15:54:08: end of X-cor INFO @ Sat, 11 Dec 2021 15:54:08: #2 finished! INFO @ Sat, 11 Dec 2021 15:54:08: #2 predicted fragment length is 146 bps INFO @ Sat, 11 Dec 2021 15:54:08: #2 alternative fragment length(s) may be 146 bps INFO @ Sat, 11 Dec 2021 15:54:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10089756/SRX10089756.05_model.r WARNING @ Sat, 11 Dec 2021 15:54:08: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:54:08: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Sat, 11 Dec 2021 15:54:08: #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 15:54:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:54:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:54:08: 2000000 INFO @ Sat, 11 Dec 2021 15:54:14: 3000000 INFO @ Sat, 11 Dec 2021 15:54:19: 4000000 INFO @ Sat, 11 Dec 2021 15:54:24: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:54:24: 5000000 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 15:54:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10089756/SRX10089756.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10089756/SRX10089756.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10089756/SRX10089756.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10089756/SRX10089756.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 15:54:27: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:54:27: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:54:30: 6000000 INFO @ Sat, 11 Dec 2021 15:54:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10089756/SRX10089756.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:54:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10089756/SRX10089756.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:54:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10089756/SRX10089756.05_summits.bed INFO @ Sat, 11 Dec 2021 15:54:32: Done! pass1 - making usageList (473 chroms): 2 millis pass2 - checking and writing primary data (5194 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:54:33: 1000000 INFO @ Sat, 11 Dec 2021 15:54:36: #1 tag size is determined as 74 bps INFO @ Sat, 11 Dec 2021 15:54:36: #1 tag size = 74 INFO @ Sat, 11 Dec 2021 15:54:36: #1 total tags in treatment: 6993655 INFO @ Sat, 11 Dec 2021 15:54:36: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:54:36: #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 15:54:37: #1 tags after filtering in treatment: 6993634 INFO @ Sat, 11 Dec 2021 15:54:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:54:37: #1 finished! INFO @ Sat, 11 Dec 2021 15:54:37: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:54:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:54:37: #2 number of paired peaks: 1453 INFO @ Sat, 11 Dec 2021 15:54:37: start model_add_line... INFO @ Sat, 11 Dec 2021 15:54:37: start X-correlation... INFO @ Sat, 11 Dec 2021 15:54:37: end of X-cor INFO @ Sat, 11 Dec 2021 15:54:37: #2 finished! INFO @ Sat, 11 Dec 2021 15:54:37: #2 predicted fragment length is 146 bps INFO @ Sat, 11 Dec 2021 15:54:37: #2 alternative fragment length(s) may be 146 bps INFO @ Sat, 11 Dec 2021 15:54:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10089756/SRX10089756.10_model.r WARNING @ Sat, 11 Dec 2021 15:54:37: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:54:37: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Sat, 11 Dec 2021 15:54:37: #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 15:54:37: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:54:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:54:39: 2000000 INFO @ Sat, 11 Dec 2021 15:54:44: 3000000 INFO @ Sat, 11 Dec 2021 15:54:50: 4000000 INFO @ Sat, 11 Dec 2021 15:54:53: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:54:55: 5000000 INFO @ Sat, 11 Dec 2021 15:55:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10089756/SRX10089756.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:55:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10089756/SRX10089756.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:55:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10089756/SRX10089756.10_summits.bed INFO @ Sat, 11 Dec 2021 15:55:00: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (407 chroms): 1 millis pass2 - checking and writing primary data (3147 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:55:01: 6000000 INFO @ Sat, 11 Dec 2021 15:55:07: #1 tag size is determined as 74 bps INFO @ Sat, 11 Dec 2021 15:55:07: #1 tag size = 74 INFO @ Sat, 11 Dec 2021 15:55:07: #1 total tags in treatment: 6993655 INFO @ Sat, 11 Dec 2021 15:55:07: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:55:07: #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 15:55:07: #1 tags after filtering in treatment: 6993634 INFO @ Sat, 11 Dec 2021 15:55:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:55:07: #1 finished! INFO @ Sat, 11 Dec 2021 15:55:07: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:55:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:55:08: #2 number of paired peaks: 1453 INFO @ Sat, 11 Dec 2021 15:55:08: start model_add_line... INFO @ Sat, 11 Dec 2021 15:55:08: start X-correlation... INFO @ Sat, 11 Dec 2021 15:55:08: end of X-cor INFO @ Sat, 11 Dec 2021 15:55:08: #2 finished! INFO @ Sat, 11 Dec 2021 15:55:08: #2 predicted fragment length is 146 bps INFO @ Sat, 11 Dec 2021 15:55:08: #2 alternative fragment length(s) may be 146 bps INFO @ Sat, 11 Dec 2021 15:55:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10089756/SRX10089756.20_model.r WARNING @ Sat, 11 Dec 2021 15:55:08: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:55:08: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Sat, 11 Dec 2021 15:55:08: #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 15:55:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:55:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:55:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:55:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10089756/SRX10089756.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:55:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10089756/SRX10089756.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:55:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10089756/SRX10089756.20_summits.bed INFO @ Sat, 11 Dec 2021 15:55:31: Done! pass1 - making usageList (308 chroms): 1 millis pass2 - checking and writing primary data (1534 records, 4 fields): 9 millis CompletedMACS2peakCalling