Job ID = 6455410 SRX = SRX287765 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:19:06 prefetch.2.10.7: 1) Downloading 'SRR869954'... 2020-06-21T10:19:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:22:09 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:22:09 prefetch.2.10.7: 1) 'SRR869954' was downloaded successfully Read 17781432 spots for SRR869954/SRR869954.sra Written 17781432 spots for SRR869954/SRR869954.sra 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: 00:05:37 17781432 reads; of these: 17781432 (100.00%) were unpaired; of these: 1098949 (6.18%) aligned 0 times 10929460 (61.47%) aligned exactly 1 time 5753023 (32.35%) aligned >1 times 93.82% overall alignment rate Time searching: 00:05:37 Overall time: 00:05:37 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] 3273003 / 16682483 = 0.1962 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 @ Sun, 21 Jun 2020 19:33:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287765/SRX287765.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287765/SRX287765.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287765/SRX287765.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287765/SRX287765.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 @ Sun, 21 Jun 2020 19:33:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:33:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:33:11: 1000000 INFO @ Sun, 21 Jun 2020 19:33:17: 2000000 INFO @ Sun, 21 Jun 2020 19:33:24: 3000000 INFO @ Sun, 21 Jun 2020 19:33:30: 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 @ Sun, 21 Jun 2020 19:33:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287765/SRX287765.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287765/SRX287765.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287765/SRX287765.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287765/SRX287765.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 @ Sun, 21 Jun 2020 19:33:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:33:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:33:36: 5000000 INFO @ Sun, 21 Jun 2020 19:33:41: 1000000 INFO @ Sun, 21 Jun 2020 19:33:43: 6000000 INFO @ Sun, 21 Jun 2020 19:33:47: 2000000 INFO @ Sun, 21 Jun 2020 19:33:49: 7000000 INFO @ Sun, 21 Jun 2020 19:33:52: 3000000 INFO @ Sun, 21 Jun 2020 19:33:56: 8000000 INFO @ Sun, 21 Jun 2020 19:33:58: 4000000 INFO @ Sun, 21 Jun 2020 19:34:03: 9000000 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 @ Sun, 21 Jun 2020 19:34:04: 5000000 INFO @ Sun, 21 Jun 2020 19:34:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287765/SRX287765.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287765/SRX287765.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287765/SRX287765.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287765/SRX287765.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 @ Sun, 21 Jun 2020 19:34:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:34:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:34:10: 10000000 INFO @ Sun, 21 Jun 2020 19:34:10: 6000000 INFO @ Sun, 21 Jun 2020 19:34:11: 1000000 INFO @ Sun, 21 Jun 2020 19:34:16: 7000000 INFO @ Sun, 21 Jun 2020 19:34:17: 11000000 INFO @ Sun, 21 Jun 2020 19:34:17: 2000000 INFO @ Sun, 21 Jun 2020 19:34:22: 8000000 INFO @ Sun, 21 Jun 2020 19:34:23: 3000000 INFO @ Sun, 21 Jun 2020 19:34:23: 12000000 INFO @ Sun, 21 Jun 2020 19:34:27: 9000000 INFO @ Sun, 21 Jun 2020 19:34:29: 4000000 INFO @ Sun, 21 Jun 2020 19:34:30: 13000000 INFO @ Sun, 21 Jun 2020 19:34:33: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:34:33: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:34:33: #1 total tags in treatment: 13409480 INFO @ Sun, 21 Jun 2020 19:34:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:34:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:34:33: #1 tags after filtering in treatment: 13409480 INFO @ Sun, 21 Jun 2020 19:34:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:34:33: #1 finished! INFO @ Sun, 21 Jun 2020 19:34:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:34:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:34:33: 10000000 INFO @ Sun, 21 Jun 2020 19:34:34: #2 number of paired peaks: 823 WARNING @ Sun, 21 Jun 2020 19:34:34: Fewer paired peaks (823) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 823 pairs to build model! INFO @ Sun, 21 Jun 2020 19:34:34: start model_add_line... INFO @ Sun, 21 Jun 2020 19:34:34: start X-correlation... INFO @ Sun, 21 Jun 2020 19:34:34: end of X-cor INFO @ Sun, 21 Jun 2020 19:34:34: #2 finished! INFO @ Sun, 21 Jun 2020 19:34:34: #2 predicted fragment length is 36 bps INFO @ Sun, 21 Jun 2020 19:34:34: #2 alternative fragment length(s) may be 3,36,555 bps INFO @ Sun, 21 Jun 2020 19:34:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287765/SRX287765.05_model.r WARNING @ Sun, 21 Jun 2020 19:34:34: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:34:34: #2 You may need to consider one of the other alternative d(s): 3,36,555 WARNING @ Sun, 21 Jun 2020 19:34:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:34:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:34:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:34:35: 5000000 INFO @ Sun, 21 Jun 2020 19:34:40: 11000000 INFO @ Sun, 21 Jun 2020 19:34:41: 6000000 INFO @ Sun, 21 Jun 2020 19:34:45: 12000000 INFO @ Sun, 21 Jun 2020 19:34:46: 7000000 INFO @ Sun, 21 Jun 2020 19:34:51: 13000000 INFO @ Sun, 21 Jun 2020 19:34:52: 8000000 INFO @ Sun, 21 Jun 2020 19:34:54: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:34:54: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:34:54: #1 total tags in treatment: 13409480 INFO @ Sun, 21 Jun 2020 19:34:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:34:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:34:54: #1 tags after filtering in treatment: 13409480 INFO @ Sun, 21 Jun 2020 19:34:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:34:54: #1 finished! INFO @ Sun, 21 Jun 2020 19:34:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:34:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:34:55: #2 number of paired peaks: 823 WARNING @ Sun, 21 Jun 2020 19:34:55: Fewer paired peaks (823) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 823 pairs to build model! INFO @ Sun, 21 Jun 2020 19:34:55: start model_add_line... INFO @ Sun, 21 Jun 2020 19:34:55: start X-correlation... INFO @ Sun, 21 Jun 2020 19:34:55: end of X-cor INFO @ Sun, 21 Jun 2020 19:34:55: #2 finished! INFO @ Sun, 21 Jun 2020 19:34:55: #2 predicted fragment length is 36 bps INFO @ Sun, 21 Jun 2020 19:34:55: #2 alternative fragment length(s) may be 3,36,555 bps INFO @ Sun, 21 Jun 2020 19:34:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287765/SRX287765.10_model.r WARNING @ Sun, 21 Jun 2020 19:34:55: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:34:55: #2 You may need to consider one of the other alternative d(s): 3,36,555 WARNING @ Sun, 21 Jun 2020 19:34:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:34:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:34:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:34:58: 9000000 INFO @ Sun, 21 Jun 2020 19:34:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:35:03: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:35:09: 11000000 INFO @ Sun, 21 Jun 2020 19:35:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287765/SRX287765.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:35:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287765/SRX287765.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:35:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287765/SRX287765.05_summits.bed INFO @ Sun, 21 Jun 2020 19:35:12: Done! pass1 - making usageList (605 chroms): 2 millis pass2 - checking and writing primary data (2338 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:35:15: 12000000 INFO @ Sun, 21 Jun 2020 19:35:20: 13000000 INFO @ Sun, 21 Jun 2020 19:35:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:35:22: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:35:22: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:35:22: #1 total tags in treatment: 13409480 INFO @ Sun, 21 Jun 2020 19:35:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:35:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:35:23: #1 tags after filtering in treatment: 13409480 INFO @ Sun, 21 Jun 2020 19:35:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:35:23: #1 finished! INFO @ Sun, 21 Jun 2020 19:35:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:35:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:35:24: #2 number of paired peaks: 823 WARNING @ Sun, 21 Jun 2020 19:35:24: Fewer paired peaks (823) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 823 pairs to build model! INFO @ Sun, 21 Jun 2020 19:35:24: start model_add_line... INFO @ Sun, 21 Jun 2020 19:35:24: start X-correlation... INFO @ Sun, 21 Jun 2020 19:35:24: end of X-cor INFO @ Sun, 21 Jun 2020 19:35:24: #2 finished! INFO @ Sun, 21 Jun 2020 19:35:24: #2 predicted fragment length is 36 bps INFO @ Sun, 21 Jun 2020 19:35:24: #2 alternative fragment length(s) may be 3,36,555 bps INFO @ Sun, 21 Jun 2020 19:35:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287765/SRX287765.20_model.r WARNING @ Sun, 21 Jun 2020 19:35:24: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:35:24: #2 You may need to consider one of the other alternative d(s): 3,36,555 WARNING @ Sun, 21 Jun 2020 19:35:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:35:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:35:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:35:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287765/SRX287765.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:35:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287765/SRX287765.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:35:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287765/SRX287765.10_summits.bed INFO @ Sun, 21 Jun 2020 19:35:34: Done! BigWig に変換しました。 pass1 - making usageList (507 chroms): 1 millis pass2 - checking and writing primary data (2031 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:35:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:36:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287765/SRX287765.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:36:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287765/SRX287765.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:36:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287765/SRX287765.20_summits.bed INFO @ Sun, 21 Jun 2020 19:36:02: Done! pass1 - making usageList (386 chroms): 1 millis pass2 - checking and writing primary data (1008 records, 4 fields): 12 millis CompletedMACS2peakCalling