Job ID = 10166604 SRX = SRX9008798 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: 00:04:33 22483228 reads; of these: 22483228 (100.00%) were unpaired; of these: 7074431 (31.47%) aligned 0 times 12764339 (56.77%) aligned exactly 1 time 2644458 (11.76%) aligned >1 times 68.53% overall alignment rate Time searching: 00:04:33 Overall time: 00:04:33 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] 5189093 / 15408797 = 0.3368 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 21:57:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9008798/SRX9008798.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9008798/SRX9008798.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9008798/SRX9008798.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9008798/SRX9008798.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 21:57:29: #1 read tag files... INFO @ Thu, 08 Oct 2020 21:57:29: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 21:57:37: 1000000 INFO @ Thu, 08 Oct 2020 21:57:44: 2000000 INFO @ Thu, 08 Oct 2020 21:57:51: 3000000 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 21:57:58: 4000000 INFO @ Thu, 08 Oct 2020 21:57:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9008798/SRX9008798.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9008798/SRX9008798.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9008798/SRX9008798.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9008798/SRX9008798.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 21:57:59: #1 read tag files... INFO @ Thu, 08 Oct 2020 21:57:59: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 21:58:06: 5000000 INFO @ Thu, 08 Oct 2020 21:58:07: 1000000 INFO @ Thu, 08 Oct 2020 21:58:14: 6000000 INFO @ Thu, 08 Oct 2020 21:58:14: 2000000 INFO @ Thu, 08 Oct 2020 21:58:22: 7000000 INFO @ Thu, 08 Oct 2020 21:58:22: 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 21:58:29: 4000000 INFO @ Thu, 08 Oct 2020 21:58:30: 8000000 INFO @ Thu, 08 Oct 2020 21:58:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9008798/SRX9008798.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9008798/SRX9008798.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9008798/SRX9008798.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9008798/SRX9008798.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 21:58:31: #1 read tag files... INFO @ Thu, 08 Oct 2020 21:58:31: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 21:58:37: 5000000 INFO @ Thu, 08 Oct 2020 21:58:39: 9000000 INFO @ Thu, 08 Oct 2020 21:58:39: 1000000 INFO @ Thu, 08 Oct 2020 21:58:45: 6000000 INFO @ Thu, 08 Oct 2020 21:58:47: 2000000 INFO @ Thu, 08 Oct 2020 21:58:47: 10000000 INFO @ Thu, 08 Oct 2020 21:58:49: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 21:58:49: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 21:58:49: #1 total tags in treatment: 10219704 INFO @ Thu, 08 Oct 2020 21:58:49: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 21:58:49: #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 21:58:49: #1 tags after filtering in treatment: 10219696 INFO @ Thu, 08 Oct 2020 21:58:49: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 21:58:49: #1 finished! INFO @ Thu, 08 Oct 2020 21:58:49: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 21:58:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 21:58:50: #2 number of paired peaks: 709 WARNING @ Thu, 08 Oct 2020 21:58:50: Fewer paired peaks (709) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 709 pairs to build model! INFO @ Thu, 08 Oct 2020 21:58:50: start model_add_line... INFO @ Thu, 08 Oct 2020 21:58:50: start X-correlation... INFO @ Thu, 08 Oct 2020 21:58:50: end of X-cor INFO @ Thu, 08 Oct 2020 21:58:50: #2 finished! INFO @ Thu, 08 Oct 2020 21:58:50: #2 predicted fragment length is 51 bps INFO @ Thu, 08 Oct 2020 21:58:50: #2 alternative fragment length(s) may be 4,51 bps INFO @ Thu, 08 Oct 2020 21:58:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9008798/SRX9008798.05_model.r WARNING @ Thu, 08 Oct 2020 21:58:50: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 21:58:50: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Thu, 08 Oct 2020 21:58:50: #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 21:58:50: #3 Call peaks... INFO @ Thu, 08 Oct 2020 21:58:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 21:58:52: 7000000 INFO @ Thu, 08 Oct 2020 21:58:54: 3000000 INFO @ Thu, 08 Oct 2020 21:59:00: 8000000 INFO @ Thu, 08 Oct 2020 21:59:01: 4000000 INFO @ Thu, 08 Oct 2020 21:59:08: 9000000 INFO @ Thu, 08 Oct 2020 21:59:08: 5000000 INFO @ Thu, 08 Oct 2020 21:59:12: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 21:59:14: 6000000 INFO @ Thu, 08 Oct 2020 21:59:15: 10000000 INFO @ Thu, 08 Oct 2020 21:59:16: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 21:59:16: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 21:59:16: #1 total tags in treatment: 10219704 INFO @ Thu, 08 Oct 2020 21:59:16: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 21:59:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 21:59:17: #1 tags after filtering in treatment: 10219696 INFO @ Thu, 08 Oct 2020 21:59:17: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 21:59:17: #1 finished! INFO @ Thu, 08 Oct 2020 21:59:17: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 21:59:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 21:59:18: #2 number of paired peaks: 709 WARNING @ Thu, 08 Oct 2020 21:59:18: Fewer paired peaks (709) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 709 pairs to build model! INFO @ Thu, 08 Oct 2020 21:59:18: start model_add_line... INFO @ Thu, 08 Oct 2020 21:59:18: start X-correlation... INFO @ Thu, 08 Oct 2020 21:59:18: end of X-cor INFO @ Thu, 08 Oct 2020 21:59:18: #2 finished! INFO @ Thu, 08 Oct 2020 21:59:18: #2 predicted fragment length is 51 bps INFO @ Thu, 08 Oct 2020 21:59:18: #2 alternative fragment length(s) may be 4,51 bps INFO @ Thu, 08 Oct 2020 21:59:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9008798/SRX9008798.10_model.r WARNING @ Thu, 08 Oct 2020 21:59:18: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 21:59:18: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Thu, 08 Oct 2020 21:59:18: #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 21:59:18: #3 Call peaks... INFO @ Thu, 08 Oct 2020 21:59:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 21:59:21: 7000000 INFO @ Thu, 08 Oct 2020 21:59:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9008798/SRX9008798.05_peaks.xls INFO @ Thu, 08 Oct 2020 21:59:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9008798/SRX9008798.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 21:59:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9008798/SRX9008798.05_summits.bed INFO @ Thu, 08 Oct 2020 21:59:23: Done! pass1 - making usageList (495 chroms): 1 millis pass2 - checking and writing primary data (4618 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 21:59:27: 8000000 INFO @ Thu, 08 Oct 2020 21:59:34: 9000000 BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 21:59:40: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 21:59:40: 10000000 INFO @ Thu, 08 Oct 2020 21:59:42: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 21:59:42: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 21:59:42: #1 total tags in treatment: 10219704 INFO @ Thu, 08 Oct 2020 21:59:42: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 21:59:42: #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 21:59:42: #1 tags after filtering in treatment: 10219696 INFO @ Thu, 08 Oct 2020 21:59:42: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 21:59:42: #1 finished! INFO @ Thu, 08 Oct 2020 21:59:42: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 21:59:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 21:59:43: #2 number of paired peaks: 709 WARNING @ Thu, 08 Oct 2020 21:59:43: Fewer paired peaks (709) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 709 pairs to build model! INFO @ Thu, 08 Oct 2020 21:59:43: start model_add_line... INFO @ Thu, 08 Oct 2020 21:59:43: start X-correlation... INFO @ Thu, 08 Oct 2020 21:59:43: end of X-cor INFO @ Thu, 08 Oct 2020 21:59:43: #2 finished! INFO @ Thu, 08 Oct 2020 21:59:43: #2 predicted fragment length is 51 bps INFO @ Thu, 08 Oct 2020 21:59:43: #2 alternative fragment length(s) may be 4,51 bps INFO @ Thu, 08 Oct 2020 21:59:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9008798/SRX9008798.20_model.r WARNING @ Thu, 08 Oct 2020 21:59:43: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 21:59:43: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Thu, 08 Oct 2020 21:59:43: #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 21:59:43: #3 Call peaks... INFO @ Thu, 08 Oct 2020 21:59:43: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 21:59:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9008798/SRX9008798.10_peaks.xls INFO @ Thu, 08 Oct 2020 21:59:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9008798/SRX9008798.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 21:59:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9008798/SRX9008798.10_summits.bed INFO @ Thu, 08 Oct 2020 21:59:52: Done! pass1 - making usageList (447 chroms): 1 millis pass2 - checking and writing primary data (2327 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 22:00:06: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 22:00:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9008798/SRX9008798.20_peaks.xls INFO @ Thu, 08 Oct 2020 22:00:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9008798/SRX9008798.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 22:00:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9008798/SRX9008798.20_summits.bed INFO @ Thu, 08 Oct 2020 22:00:17: Done! pass1 - making usageList (355 chroms): 1 millis pass2 - checking and writing primary data (898 records, 4 fields): 10 millis CompletedMACS2peakCalling