Job ID = 14172014 SRX = SRX9008801 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: 00:06:26 30139461 reads; of these: 30139461 (100.00%) were unpaired; of these: 11644620 (38.64%) aligned 0 times 14679643 (48.71%) aligned exactly 1 time 3815198 (12.66%) aligned >1 times 61.36% overall alignment rate Time searching: 00:06:26 Overall time: 00:06:26 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 8 files... [bam_rmdupse_core] 3330444 / 18494841 = 0.1801 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 13:57:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.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 13:57:35: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:57:35: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:57:40: 1000000 INFO @ Sat, 11 Dec 2021 13:57:46: 2000000 INFO @ Sat, 11 Dec 2021 13:57:51: 3000000 INFO @ Sat, 11 Dec 2021 13:57:56: 4000000 INFO @ Sat, 11 Dec 2021 13:58:01: 5000000 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 13:58:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.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 13:58:05: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:58:05: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:58:07: 6000000 INFO @ Sat, 11 Dec 2021 13:58:11: 1000000 INFO @ Sat, 11 Dec 2021 13:58:12: 7000000 INFO @ Sat, 11 Dec 2021 13:58:16: 2000000 INFO @ Sat, 11 Dec 2021 13:58:18: 8000000 INFO @ Sat, 11 Dec 2021 13:58:22: 3000000 INFO @ Sat, 11 Dec 2021 13:58:24: 9000000 INFO @ Sat, 11 Dec 2021 13:58:27: 4000000 INFO @ Sat, 11 Dec 2021 13:58:29: 10000000 INFO @ Sat, 11 Dec 2021 13:58:33: 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 13:58:35: 11000000 INFO @ Sat, 11 Dec 2021 13:58:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.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 13:58:36: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:58:36: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:58:39: 6000000 INFO @ Sat, 11 Dec 2021 13:58:40: 12000000 INFO @ Sat, 11 Dec 2021 13:58:42: 1000000 INFO @ Sat, 11 Dec 2021 13:58:45: 7000000 INFO @ Sat, 11 Dec 2021 13:58:46: 13000000 INFO @ Sat, 11 Dec 2021 13:58:48: 2000000 INFO @ Sat, 11 Dec 2021 13:58:51: 8000000 INFO @ Sat, 11 Dec 2021 13:58:51: 14000000 INFO @ Sat, 11 Dec 2021 13:58:54: 3000000 INFO @ Sat, 11 Dec 2021 13:58:57: 9000000 INFO @ Sat, 11 Dec 2021 13:58:57: 15000000 INFO @ Sat, 11 Dec 2021 13:58:59: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:58:59: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:58:59: #1 total tags in treatment: 15164397 INFO @ Sat, 11 Dec 2021 13:58:59: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:58:59: #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 13:59:00: #1 tags after filtering in treatment: 15164393 INFO @ Sat, 11 Dec 2021 13:59:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:59:00: #1 finished! INFO @ Sat, 11 Dec 2021 13:59:00: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:59:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:59:01: 4000000 INFO @ Sat, 11 Dec 2021 13:59:01: #2 number of paired peaks: 598 WARNING @ Sat, 11 Dec 2021 13:59:01: Fewer paired peaks (598) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 598 pairs to build model! INFO @ Sat, 11 Dec 2021 13:59:01: start model_add_line... INFO @ Sat, 11 Dec 2021 13:59:01: start X-correlation... INFO @ Sat, 11 Dec 2021 13:59:01: end of X-cor INFO @ Sat, 11 Dec 2021 13:59:01: #2 finished! INFO @ Sat, 11 Dec 2021 13:59:01: #2 predicted fragment length is 42 bps INFO @ Sat, 11 Dec 2021 13:59:01: #2 alternative fragment length(s) may be 2,42 bps INFO @ Sat, 11 Dec 2021 13:59:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.05_model.r WARNING @ Sat, 11 Dec 2021 13:59:01: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:59:01: #2 You may need to consider one of the other alternative d(s): 2,42 WARNING @ Sat, 11 Dec 2021 13:59:01: #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 13:59:01: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:59:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:59:03: 10000000 INFO @ Sat, 11 Dec 2021 13:59:07: 5000000 INFO @ Sat, 11 Dec 2021 13:59:09: 11000000 INFO @ Sat, 11 Dec 2021 13:59:13: 6000000 INFO @ Sat, 11 Dec 2021 13:59:15: 12000000 INFO @ Sat, 11 Dec 2021 13:59:19: 7000000 INFO @ Sat, 11 Dec 2021 13:59:22: 13000000 INFO @ Sat, 11 Dec 2021 13:59:25: 8000000 INFO @ Sat, 11 Dec 2021 13:59:27: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:59:28: 14000000 INFO @ Sat, 11 Dec 2021 13:59:31: 9000000 INFO @ Sat, 11 Dec 2021 13:59:35: 15000000 INFO @ Sat, 11 Dec 2021 13:59:36: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:59:36: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:59:36: #1 total tags in treatment: 15164397 INFO @ Sat, 11 Dec 2021 13:59:36: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:59:36: #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 13:59:37: 10000000 INFO @ Sat, 11 Dec 2021 13:59:37: #1 tags after filtering in treatment: 15164393 INFO @ Sat, 11 Dec 2021 13:59:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 13:59:37: #1 finished! INFO @ Sat, 11 Dec 2021 13:59:37: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:59:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:59:38: #2 number of paired peaks: 598 WARNING @ Sat, 11 Dec 2021 13:59:38: Fewer paired peaks (598) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 598 pairs to build model! INFO @ Sat, 11 Dec 2021 13:59:38: start model_add_line... INFO @ Sat, 11 Dec 2021 13:59:38: start X-correlation... INFO @ Sat, 11 Dec 2021 13:59:38: end of X-cor INFO @ Sat, 11 Dec 2021 13:59:38: #2 finished! INFO @ Sat, 11 Dec 2021 13:59:38: #2 predicted fragment length is 42 bps INFO @ Sat, 11 Dec 2021 13:59:38: #2 alternative fragment length(s) may be 2,42 bps INFO @ Sat, 11 Dec 2021 13:59:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.10_model.r WARNING @ Sat, 11 Dec 2021 13:59:38: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:59:38: #2 You may need to consider one of the other alternative d(s): 2,42 WARNING @ Sat, 11 Dec 2021 13:59:38: #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 13:59:38: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:59:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:59:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:59:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:59:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.05_summits.bed INFO @ Sat, 11 Dec 2021 13:59:42: Done! INFO @ Sat, 11 Dec 2021 13:59:42: 11000000 pass1 - making usageList (524 chroms): 6 millis pass2 - checking and writing primary data (2028 records, 4 fields): 49 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:59:48: 12000000 INFO @ Sat, 11 Dec 2021 13:59:54: 13000000 INFO @ Sat, 11 Dec 2021 13:59:59: 14000000 INFO @ Sat, 11 Dec 2021 14:00:05: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:00:05: 15000000 INFO @ Sat, 11 Dec 2021 14:00:07: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:00:07: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:00:07: #1 total tags in treatment: 15164397 INFO @ Sat, 11 Dec 2021 14:00:07: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:00:07: #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 14:00:07: #1 tags after filtering in treatment: 15164393 INFO @ Sat, 11 Dec 2021 14:00:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 14:00:07: #1 finished! INFO @ Sat, 11 Dec 2021 14:00:07: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:00:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:00:08: #2 number of paired peaks: 598 WARNING @ Sat, 11 Dec 2021 14:00:08: Fewer paired peaks (598) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 598 pairs to build model! INFO @ Sat, 11 Dec 2021 14:00:08: start model_add_line... INFO @ Sat, 11 Dec 2021 14:00:08: start X-correlation... INFO @ Sat, 11 Dec 2021 14:00:08: end of X-cor INFO @ Sat, 11 Dec 2021 14:00:08: #2 finished! INFO @ Sat, 11 Dec 2021 14:00:08: #2 predicted fragment length is 42 bps INFO @ Sat, 11 Dec 2021 14:00:08: #2 alternative fragment length(s) may be 2,42 bps INFO @ Sat, 11 Dec 2021 14:00:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.20_model.r WARNING @ Sat, 11 Dec 2021 14:00:08: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:00:08: #2 You may need to consider one of the other alternative d(s): 2,42 WARNING @ Sat, 11 Dec 2021 14:00:08: #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 14:00:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:00:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:00:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:00:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:00:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.10_summits.bed INFO @ Sat, 11 Dec 2021 14:00:20: Done! pass1 - making usageList (445 chroms): 1 millis pass2 - checking and writing primary data (1738 records, 4 fields): 33 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:00:35: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:00:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:00:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:00:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.20_summits.bed INFO @ Sat, 11 Dec 2021 14:00:49: Done! pass1 - making usageList (350 chroms): 2 millis pass2 - checking and writing primary data (948 records, 4 fields): 23 millis CompletedMACS2peakCalling BigWig に変換しました。