Job ID = 16438060 SRX = SRX12261324 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: 00:11:25 27583319 reads; of these: 27583319 (100.00%) were unpaired; of these: 1495858 (5.42%) aligned 0 times 18031174 (65.37%) aligned exactly 1 time 8056287 (29.21%) aligned >1 times 94.58% overall alignment rate Time searching: 00:11:25 Overall time: 00:11:25 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] 14880165 / 26087461 = 0.5704 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 13:43:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX12261324/SRX12261324.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX12261324/SRX12261324.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX12261324/SRX12261324.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX12261324/SRX12261324.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 13:43:55: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:43:55: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:44:03: 1000000 INFO @ Tue, 02 Aug 2022 13:44:11: 2000000 INFO @ Tue, 02 Aug 2022 13:44:18: 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 13:44:25: 4000000 INFO @ Tue, 02 Aug 2022 13:44:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX12261324/SRX12261324.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX12261324/SRX12261324.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX12261324/SRX12261324.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX12261324/SRX12261324.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 13:44:25: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:44:25: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:44:33: 5000000 INFO @ Tue, 02 Aug 2022 13:44:33: 1000000 INFO @ Tue, 02 Aug 2022 13:44:41: 6000000 INFO @ Tue, 02 Aug 2022 13:44:41: 2000000 INFO @ Tue, 02 Aug 2022 13:44:49: 7000000 INFO @ Tue, 02 Aug 2022 13:44:49: 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 13:44:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX12261324/SRX12261324.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX12261324/SRX12261324.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX12261324/SRX12261324.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX12261324/SRX12261324.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 13:44:55: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:44:55: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:44:57: 8000000 INFO @ Tue, 02 Aug 2022 13:44:58: 4000000 INFO @ Tue, 02 Aug 2022 13:45:05: 1000000 INFO @ Tue, 02 Aug 2022 13:45:06: 9000000 INFO @ Tue, 02 Aug 2022 13:45:06: 5000000 INFO @ Tue, 02 Aug 2022 13:45:14: 10000000 INFO @ Tue, 02 Aug 2022 13:45:14: 2000000 INFO @ Tue, 02 Aug 2022 13:45:15: 6000000 INFO @ Tue, 02 Aug 2022 13:45:23: 11000000 INFO @ Tue, 02 Aug 2022 13:45:23: 7000000 INFO @ Tue, 02 Aug 2022 13:45:24: 3000000 INFO @ Tue, 02 Aug 2022 13:45:25: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:45:25: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:45:25: #1 total tags in treatment: 11207296 INFO @ Tue, 02 Aug 2022 13:45:25: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:45:25: #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 13:45:25: #1 tags after filtering in treatment: 11207294 INFO @ Tue, 02 Aug 2022 13:45:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:45:25: #1 finished! INFO @ Tue, 02 Aug 2022 13:45:25: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:45:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:45:26: #2 number of paired peaks: 1308 INFO @ Tue, 02 Aug 2022 13:45:26: start model_add_line... INFO @ Tue, 02 Aug 2022 13:45:26: start X-correlation... INFO @ Tue, 02 Aug 2022 13:45:26: end of X-cor INFO @ Tue, 02 Aug 2022 13:45:26: #2 finished! INFO @ Tue, 02 Aug 2022 13:45:26: #2 predicted fragment length is 86 bps INFO @ Tue, 02 Aug 2022 13:45:26: #2 alternative fragment length(s) may be 86 bps INFO @ Tue, 02 Aug 2022 13:45:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX12261324/SRX12261324.05_model.r WARNING @ Tue, 02 Aug 2022 13:45:27: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:45:27: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Tue, 02 Aug 2022 13:45:27: #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 13:45:27: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:45:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:45:32: 8000000 INFO @ Tue, 02 Aug 2022 13:45:34: 4000000 INFO @ Tue, 02 Aug 2022 13:45:41: 9000000 INFO @ Tue, 02 Aug 2022 13:45:43: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:45:49: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:45:49: 10000000 INFO @ Tue, 02 Aug 2022 13:45:52: 6000000 INFO @ Tue, 02 Aug 2022 13:45:58: 11000000 INFO @ Tue, 02 Aug 2022 13:46:00: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:46:00: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:46:00: #1 total tags in treatment: 11207296 INFO @ Tue, 02 Aug 2022 13:46:00: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:46:00: #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 13:46:00: #1 tags after filtering in treatment: 11207294 INFO @ Tue, 02 Aug 2022 13:46:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:46:00: #1 finished! INFO @ Tue, 02 Aug 2022 13:46:00: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:46:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:46:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX12261324/SRX12261324.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:46:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX12261324/SRX12261324.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:46:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX12261324/SRX12261324.05_summits.bed INFO @ Tue, 02 Aug 2022 13:46:00: Done! pass1 - making usageList (775 chroms): 2 millis INFO @ Tue, 02 Aug 2022 13:46:01: #2 number of paired peaks: 1308 INFO @ Tue, 02 Aug 2022 13:46:01: start model_add_line... pass2 - checking and writing primary data (8146 records, 4 fields): 47 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:46:01: start X-correlation... INFO @ Tue, 02 Aug 2022 13:46:01: end of X-cor INFO @ Tue, 02 Aug 2022 13:46:01: #2 finished! INFO @ Tue, 02 Aug 2022 13:46:01: #2 predicted fragment length is 86 bps INFO @ Tue, 02 Aug 2022 13:46:01: #2 alternative fragment length(s) may be 86 bps INFO @ Tue, 02 Aug 2022 13:46:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX12261324/SRX12261324.10_model.r WARNING @ Tue, 02 Aug 2022 13:46:01: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:46:01: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Tue, 02 Aug 2022 13:46:01: #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 13:46:01: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:46:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:46:01: 7000000 INFO @ Tue, 02 Aug 2022 13:46:10: 8000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:46:18: 9000000 INFO @ Tue, 02 Aug 2022 13:46:23: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:46:26: 10000000 INFO @ Tue, 02 Aug 2022 13:46:35: 11000000 INFO @ Tue, 02 Aug 2022 13:46:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX12261324/SRX12261324.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:46:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX12261324/SRX12261324.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:46:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX12261324/SRX12261324.10_summits.bed INFO @ Tue, 02 Aug 2022 13:46:35: Done! pass1 - making usageList (611 chroms): 1 millis INFO @ Tue, 02 Aug 2022 13:46:36: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:46:36: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:46:36: #1 total tags in treatment: 11207296 INFO @ Tue, 02 Aug 2022 13:46:36: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:46:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass2 - checking and writing primary data (3916 records, 4 fields): 65 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:46:37: #1 tags after filtering in treatment: 11207294 INFO @ Tue, 02 Aug 2022 13:46:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:46:37: #1 finished! INFO @ Tue, 02 Aug 2022 13:46:37: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:46:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:46:37: #2 number of paired peaks: 1308 INFO @ Tue, 02 Aug 2022 13:46:37: start model_add_line... INFO @ Tue, 02 Aug 2022 13:46:38: start X-correlation... INFO @ Tue, 02 Aug 2022 13:46:38: end of X-cor INFO @ Tue, 02 Aug 2022 13:46:38: #2 finished! INFO @ Tue, 02 Aug 2022 13:46:38: #2 predicted fragment length is 86 bps INFO @ Tue, 02 Aug 2022 13:46:38: #2 alternative fragment length(s) may be 86 bps INFO @ Tue, 02 Aug 2022 13:46:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX12261324/SRX12261324.20_model.r WARNING @ Tue, 02 Aug 2022 13:46:38: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:46:38: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Tue, 02 Aug 2022 13:46:38: #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 13:46:38: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:46:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:47:00: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:47:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX12261324/SRX12261324.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:47:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX12261324/SRX12261324.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:47:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX12261324/SRX12261324.20_summits.bed INFO @ Tue, 02 Aug 2022 13:47:12: Done! pass1 - making usageList (517 chroms): 1 millis pass2 - checking and writing primary data (1825 records, 4 fields): 33 millis CompletedMACS2peakCalling