Job ID = 6529258 SRX = SRX111782 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: 00:04:48 17232507 reads; of these: 17232507 (100.00%) were unpaired; of these: 337974 (1.96%) aligned 0 times 12617078 (73.22%) aligned exactly 1 time 4277455 (24.82%) aligned >1 times 98.04% overall alignment rate Time searching: 00:04:48 Overall time: 00:04:48 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] 3804799 / 16894533 = 0.2252 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 @ Tue, 30 Jun 2020 01:56:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX111782/SRX111782.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX111782/SRX111782.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX111782/SRX111782.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX111782/SRX111782.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, 30 Jun 2020 01:56:46: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:56:46: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:56:52: 1000000 INFO @ Tue, 30 Jun 2020 01:56:58: 2000000 INFO @ Tue, 30 Jun 2020 01:57:04: 3000000 INFO @ Tue, 30 Jun 2020 01:57:10: 4000000 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 @ Tue, 30 Jun 2020 01:57:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX111782/SRX111782.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX111782/SRX111782.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX111782/SRX111782.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX111782/SRX111782.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, 30 Jun 2020 01:57:16: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:57:16: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:57:16: 5000000 INFO @ Tue, 30 Jun 2020 01:57:22: 1000000 INFO @ Tue, 30 Jun 2020 01:57:23: 6000000 INFO @ Tue, 30 Jun 2020 01:57:29: 2000000 INFO @ Tue, 30 Jun 2020 01:57:29: 7000000 INFO @ Tue, 30 Jun 2020 01:57:36: 8000000 INFO @ Tue, 30 Jun 2020 01:57:36: 3000000 INFO @ Tue, 30 Jun 2020 01:57:42: 9000000 INFO @ Tue, 30 Jun 2020 01:57:42: 4000000 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 @ Tue, 30 Jun 2020 01:57:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX111782/SRX111782.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX111782/SRX111782.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX111782/SRX111782.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX111782/SRX111782.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, 30 Jun 2020 01:57:46: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:57:46: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:57:49: 10000000 INFO @ Tue, 30 Jun 2020 01:57:49: 5000000 INFO @ Tue, 30 Jun 2020 01:57:53: 1000000 INFO @ Tue, 30 Jun 2020 01:57:56: 6000000 INFO @ Tue, 30 Jun 2020 01:57:56: 11000000 INFO @ Tue, 30 Jun 2020 01:58:00: 2000000 INFO @ Tue, 30 Jun 2020 01:58:02: 7000000 INFO @ Tue, 30 Jun 2020 01:58:03: 12000000 INFO @ Tue, 30 Jun 2020 01:58:06: 3000000 INFO @ Tue, 30 Jun 2020 01:58:09: 8000000 INFO @ Tue, 30 Jun 2020 01:58:10: 13000000 INFO @ Tue, 30 Jun 2020 01:58:10: #1 tag size is determined as 44 bps INFO @ Tue, 30 Jun 2020 01:58:10: #1 tag size = 44 INFO @ Tue, 30 Jun 2020 01:58:10: #1 total tags in treatment: 13089734 INFO @ Tue, 30 Jun 2020 01:58:10: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:58:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:58:11: #1 tags after filtering in treatment: 13089733 INFO @ Tue, 30 Jun 2020 01:58:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:58:11: #1 finished! INFO @ Tue, 30 Jun 2020 01:58:11: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:58:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:58:12: #2 number of paired peaks: 128 WARNING @ Tue, 30 Jun 2020 01:58:12: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Tue, 30 Jun 2020 01:58:12: start model_add_line... INFO @ Tue, 30 Jun 2020 01:58:12: start X-correlation... INFO @ Tue, 30 Jun 2020 01:58:12: end of X-cor INFO @ Tue, 30 Jun 2020 01:58:12: #2 finished! INFO @ Tue, 30 Jun 2020 01:58:12: #2 predicted fragment length is 48 bps INFO @ Tue, 30 Jun 2020 01:58:12: #2 alternative fragment length(s) may be 4,48,56,485,577 bps INFO @ Tue, 30 Jun 2020 01:58:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX111782/SRX111782.05_model.r WARNING @ Tue, 30 Jun 2020 01:58:12: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:58:12: #2 You may need to consider one of the other alternative d(s): 4,48,56,485,577 WARNING @ Tue, 30 Jun 2020 01:58:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:58:12: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:58:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:58:13: 4000000 INFO @ Tue, 30 Jun 2020 01:58:15: 9000000 INFO @ Tue, 30 Jun 2020 01:58:19: 5000000 INFO @ Tue, 30 Jun 2020 01:58:21: 10000000 INFO @ Tue, 30 Jun 2020 01:58:26: 6000000 INFO @ Tue, 30 Jun 2020 01:58:28: 11000000 INFO @ Tue, 30 Jun 2020 01:58:32: 7000000 INFO @ Tue, 30 Jun 2020 01:58:35: 12000000 INFO @ Tue, 30 Jun 2020 01:58:39: 8000000 INFO @ Tue, 30 Jun 2020 01:58:41: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:58:42: 13000000 INFO @ Tue, 30 Jun 2020 01:58:42: #1 tag size is determined as 44 bps INFO @ Tue, 30 Jun 2020 01:58:42: #1 tag size = 44 INFO @ Tue, 30 Jun 2020 01:58:42: #1 total tags in treatment: 13089734 INFO @ Tue, 30 Jun 2020 01:58:42: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:58:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:58:43: #1 tags after filtering in treatment: 13089733 INFO @ Tue, 30 Jun 2020 01:58:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:58:43: #1 finished! INFO @ Tue, 30 Jun 2020 01:58:43: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:58:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:58:44: #2 number of paired peaks: 128 WARNING @ Tue, 30 Jun 2020 01:58:44: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Tue, 30 Jun 2020 01:58:44: start model_add_line... INFO @ Tue, 30 Jun 2020 01:58:44: start X-correlation... INFO @ Tue, 30 Jun 2020 01:58:44: end of X-cor INFO @ Tue, 30 Jun 2020 01:58:44: #2 finished! INFO @ Tue, 30 Jun 2020 01:58:44: #2 predicted fragment length is 48 bps INFO @ Tue, 30 Jun 2020 01:58:44: #2 alternative fragment length(s) may be 4,48,56,485,577 bps INFO @ Tue, 30 Jun 2020 01:58:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX111782/SRX111782.10_model.r WARNING @ Tue, 30 Jun 2020 01:58:44: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:58:44: #2 You may need to consider one of the other alternative d(s): 4,48,56,485,577 WARNING @ Tue, 30 Jun 2020 01:58:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:58:44: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:58:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:58:45: 9000000 INFO @ Tue, 30 Jun 2020 01:58:51: 10000000 INFO @ Tue, 30 Jun 2020 01:58:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX111782/SRX111782.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:58:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX111782/SRX111782.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:58:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX111782/SRX111782.05_summits.bed INFO @ Tue, 30 Jun 2020 01:58:55: Done! pass1 - making usageList (218 chroms): 1 millis pass2 - checking and writing primary data (510 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:58:58: 11000000 INFO @ Tue, 30 Jun 2020 01:59:04: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:59:10: 13000000 INFO @ Tue, 30 Jun 2020 01:59:10: #1 tag size is determined as 44 bps INFO @ Tue, 30 Jun 2020 01:59:10: #1 tag size = 44 INFO @ Tue, 30 Jun 2020 01:59:10: #1 total tags in treatment: 13089734 INFO @ Tue, 30 Jun 2020 01:59:10: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:59:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:59:11: #1 tags after filtering in treatment: 13089733 INFO @ Tue, 30 Jun 2020 01:59:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:59:11: #1 finished! INFO @ Tue, 30 Jun 2020 01:59:11: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:59:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:59:12: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:59:12: #2 number of paired peaks: 128 WARNING @ Tue, 30 Jun 2020 01:59:12: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Tue, 30 Jun 2020 01:59:12: start model_add_line... INFO @ Tue, 30 Jun 2020 01:59:12: start X-correlation... INFO @ Tue, 30 Jun 2020 01:59:12: end of X-cor INFO @ Tue, 30 Jun 2020 01:59:12: #2 finished! INFO @ Tue, 30 Jun 2020 01:59:12: #2 predicted fragment length is 48 bps INFO @ Tue, 30 Jun 2020 01:59:12: #2 alternative fragment length(s) may be 4,48,56,485,577 bps INFO @ Tue, 30 Jun 2020 01:59:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX111782/SRX111782.20_model.r WARNING @ Tue, 30 Jun 2020 01:59:12: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:59:12: #2 You may need to consider one of the other alternative d(s): 4,48,56,485,577 WARNING @ Tue, 30 Jun 2020 01:59:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:59:12: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:59:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:59:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX111782/SRX111782.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:59:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX111782/SRX111782.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:59:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX111782/SRX111782.10_summits.bed INFO @ Tue, 30 Jun 2020 01:59:26: Done! pass1 - making usageList (98 chroms): 1 millis pass2 - checking and writing primary data (242 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:59:39: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:59:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX111782/SRX111782.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:59:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX111782/SRX111782.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:59:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX111782/SRX111782.20_summits.bed INFO @ Tue, 30 Jun 2020 01:59:53: Done! pass1 - making usageList (66 chroms): 1 millis pass2 - checking and writing primary data (128 records, 4 fields): 3 millis CompletedMACS2peakCalling