Job ID = 16438080 SRX = SRX12261335 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: 00:11:11 21108005 reads; of these: 21108005 (100.00%) were unpaired; of these: 1152223 (5.46%) aligned 0 times 12484701 (59.15%) aligned exactly 1 time 7471081 (35.39%) aligned >1 times 94.54% overall alignment rate Time searching: 00:11:11 Overall time: 00:11:11 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] 5694039 / 19955782 = 0.2853 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 13:48:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX12261335/SRX12261335.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX12261335/SRX12261335.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX12261335/SRX12261335.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX12261335/SRX12261335.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 13:48:39: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:48:39: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:48:47: 1000000 INFO @ Tue, 02 Aug 2022 13:48:56: 2000000 INFO @ Tue, 02 Aug 2022 13:49:03: 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 13:49:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX12261335/SRX12261335.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX12261335/SRX12261335.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX12261335/SRX12261335.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX12261335/SRX12261335.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 13:49:09: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:49:09: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:49:11: 4000000 INFO @ Tue, 02 Aug 2022 13:49:17: 1000000 INFO @ Tue, 02 Aug 2022 13:49:19: 5000000 INFO @ Tue, 02 Aug 2022 13:49:26: 2000000 INFO @ Tue, 02 Aug 2022 13:49:27: 6000000 INFO @ Tue, 02 Aug 2022 13:49:34: 3000000 INFO @ Tue, 02 Aug 2022 13:49:35: 7000000 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 13:49:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX12261335/SRX12261335.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX12261335/SRX12261335.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX12261335/SRX12261335.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX12261335/SRX12261335.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 13:49:39: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:49:39: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:49:42: 4000000 INFO @ Tue, 02 Aug 2022 13:49:44: 8000000 INFO @ Tue, 02 Aug 2022 13:49:48: 1000000 INFO @ Tue, 02 Aug 2022 13:49:50: 5000000 INFO @ Tue, 02 Aug 2022 13:49:52: 9000000 INFO @ Tue, 02 Aug 2022 13:49:56: 2000000 INFO @ Tue, 02 Aug 2022 13:49:59: 6000000 INFO @ Tue, 02 Aug 2022 13:50:01: 10000000 INFO @ Tue, 02 Aug 2022 13:50:05: 3000000 INFO @ Tue, 02 Aug 2022 13:50:07: 7000000 INFO @ Tue, 02 Aug 2022 13:50:09: 11000000 INFO @ Tue, 02 Aug 2022 13:50:13: 4000000 INFO @ Tue, 02 Aug 2022 13:50:16: 8000000 INFO @ Tue, 02 Aug 2022 13:50:18: 12000000 INFO @ Tue, 02 Aug 2022 13:50:22: 5000000 INFO @ Tue, 02 Aug 2022 13:50:24: 9000000 INFO @ Tue, 02 Aug 2022 13:50:27: 13000000 INFO @ Tue, 02 Aug 2022 13:50:30: 6000000 INFO @ Tue, 02 Aug 2022 13:50:33: 10000000 INFO @ Tue, 02 Aug 2022 13:50:36: 14000000 INFO @ Tue, 02 Aug 2022 13:50:38: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:50:38: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:50:38: #1 total tags in treatment: 14261743 INFO @ Tue, 02 Aug 2022 13:50:38: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:50:38: #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 13:50:39: 7000000 INFO @ Tue, 02 Aug 2022 13:50:39: #1 tags after filtering in treatment: 14261740 INFO @ Tue, 02 Aug 2022 13:50:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:50:39: #1 finished! INFO @ Tue, 02 Aug 2022 13:50:39: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:50:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:50:40: #2 number of paired peaks: 875 WARNING @ Tue, 02 Aug 2022 13:50:40: Fewer paired peaks (875) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 875 pairs to build model! INFO @ Tue, 02 Aug 2022 13:50:40: start model_add_line... INFO @ Tue, 02 Aug 2022 13:50:40: start X-correlation... INFO @ Tue, 02 Aug 2022 13:50:40: end of X-cor INFO @ Tue, 02 Aug 2022 13:50:40: #2 finished! INFO @ Tue, 02 Aug 2022 13:50:40: #2 predicted fragment length is 63 bps INFO @ Tue, 02 Aug 2022 13:50:40: #2 alternative fragment length(s) may be 4,63 bps INFO @ Tue, 02 Aug 2022 13:50:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX12261335/SRX12261335.05_model.r WARNING @ Tue, 02 Aug 2022 13:50:40: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:50:40: #2 You may need to consider one of the other alternative d(s): 4,63 WARNING @ Tue, 02 Aug 2022 13:50:40: #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 13:50:40: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:50:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:50:41: 11000000 INFO @ Tue, 02 Aug 2022 13:50:47: 8000000 INFO @ Tue, 02 Aug 2022 13:50:50: 12000000 INFO @ Tue, 02 Aug 2022 13:50:55: 9000000 INFO @ Tue, 02 Aug 2022 13:50:58: 13000000 INFO @ Tue, 02 Aug 2022 13:51:03: 10000000 INFO @ Tue, 02 Aug 2022 13:51:06: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:51:07: 14000000 INFO @ Tue, 02 Aug 2022 13:51:09: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:51:09: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:51:09: #1 total tags in treatment: 14261743 INFO @ Tue, 02 Aug 2022 13:51:09: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:51:09: #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 13:51:10: #1 tags after filtering in treatment: 14261740 INFO @ Tue, 02 Aug 2022 13:51:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:51:10: #1 finished! INFO @ Tue, 02 Aug 2022 13:51:10: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:51:10: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:51:11: #2 number of paired peaks: 875 WARNING @ Tue, 02 Aug 2022 13:51:11: Fewer paired peaks (875) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 875 pairs to build model! INFO @ Tue, 02 Aug 2022 13:51:11: start model_add_line... INFO @ Tue, 02 Aug 2022 13:51:11: 11000000 INFO @ Tue, 02 Aug 2022 13:51:11: start X-correlation... INFO @ Tue, 02 Aug 2022 13:51:11: end of X-cor INFO @ Tue, 02 Aug 2022 13:51:11: #2 finished! INFO @ Tue, 02 Aug 2022 13:51:11: #2 predicted fragment length is 63 bps INFO @ Tue, 02 Aug 2022 13:51:11: #2 alternative fragment length(s) may be 4,63 bps INFO @ Tue, 02 Aug 2022 13:51:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX12261335/SRX12261335.10_model.r WARNING @ Tue, 02 Aug 2022 13:51:11: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:51:11: #2 You may need to consider one of the other alternative d(s): 4,63 WARNING @ Tue, 02 Aug 2022 13:51:11: #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 13:51:11: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:51:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:51:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX12261335/SRX12261335.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:51:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX12261335/SRX12261335.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:51:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX12261335/SRX12261335.05_summits.bed INFO @ Tue, 02 Aug 2022 13:51:19: Done! INFO @ Tue, 02 Aug 2022 13:51:19: 12000000 pass1 - making usageList (698 chroms): 2 millis pass2 - checking and writing primary data (2394 records, 4 fields): 73 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:51:27: 13000000 INFO @ Tue, 02 Aug 2022 13:51:34: 14000000 INFO @ Tue, 02 Aug 2022 13:51:36: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:51:36: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:51:36: #1 total tags in treatment: 14261743 INFO @ Tue, 02 Aug 2022 13:51:36: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:51:36: #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 13:51:37: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:51:37: #1 tags after filtering in treatment: 14261740 INFO @ Tue, 02 Aug 2022 13:51:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:51:37: #1 finished! INFO @ Tue, 02 Aug 2022 13:51:37: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:51:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:51:38: #2 number of paired peaks: 875 WARNING @ Tue, 02 Aug 2022 13:51:38: Fewer paired peaks (875) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 875 pairs to build model! INFO @ Tue, 02 Aug 2022 13:51:38: start model_add_line... INFO @ Tue, 02 Aug 2022 13:51:38: start X-correlation... INFO @ Tue, 02 Aug 2022 13:51:38: end of X-cor INFO @ Tue, 02 Aug 2022 13:51:38: #2 finished! INFO @ Tue, 02 Aug 2022 13:51:38: #2 predicted fragment length is 63 bps INFO @ Tue, 02 Aug 2022 13:51:38: #2 alternative fragment length(s) may be 4,63 bps INFO @ Tue, 02 Aug 2022 13:51:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX12261335/SRX12261335.20_model.r WARNING @ Tue, 02 Aug 2022 13:51:38: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:51:38: #2 You may need to consider one of the other alternative d(s): 4,63 WARNING @ Tue, 02 Aug 2022 13:51:38: #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 13:51:38: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:51:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:51:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX12261335/SRX12261335.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:51:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX12261335/SRX12261335.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:51:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX12261335/SRX12261335.10_summits.bed INFO @ Tue, 02 Aug 2022 13:51:50: Done! BigWig に変換しました。 pass1 - making usageList (588 chroms): 2 millis pass2 - checking and writing primary data (1666 records, 4 fields): 54 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:52:04: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:52:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX12261335/SRX12261335.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:52:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX12261335/SRX12261335.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:52:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX12261335/SRX12261335.20_summits.bed INFO @ Tue, 02 Aug 2022 13:52:18: Done! pass1 - making usageList (506 chroms): 2 millis pass2 - checking and writing primary data (1394 records, 4 fields): 49 millis CompletedMACS2peakCalling