Job ID = 6454042 SRX = SRX1794227 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:48:38 prefetch.2.10.7: 1) Downloading 'SRR3575264'... 2020-06-21T08:48:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:49:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:49:57 prefetch.2.10.7: 'SRR3575264' is valid 2020-06-21T08:49:57 prefetch.2.10.7: 1) 'SRR3575264' was downloaded successfully Read 10164975 spots for SRR3575264/SRR3575264.sra Written 10164975 spots for SRR3575264/SRR3575264.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: 00:02:49 10164975 reads; of these: 10164975 (100.00%) were unpaired; of these: 323108 (3.18%) aligned 0 times 7349821 (72.31%) aligned exactly 1 time 2492046 (24.52%) aligned >1 times 96.82% overall alignment rate Time searching: 00:02:49 Overall time: 00:02:49 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] 508529 / 9841867 = 0.0517 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 17:56:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1794227/SRX1794227.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1794227/SRX1794227.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1794227/SRX1794227.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1794227/SRX1794227.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 17:56:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:56:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:56:35: 1000000 INFO @ Sun, 21 Jun 2020 17:56:41: 2000000 INFO @ Sun, 21 Jun 2020 17:56:46: 3000000 INFO @ Sun, 21 Jun 2020 17:56:51: 4000000 INFO @ Sun, 21 Jun 2020 17:56:56: 5000000 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 17:57:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1794227/SRX1794227.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1794227/SRX1794227.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1794227/SRX1794227.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1794227/SRX1794227.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 17:57:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:57:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:57:02: 6000000 INFO @ Sun, 21 Jun 2020 17:57:06: 1000000 INFO @ Sun, 21 Jun 2020 17:57:07: 7000000 INFO @ Sun, 21 Jun 2020 17:57:11: 2000000 INFO @ Sun, 21 Jun 2020 17:57:12: 8000000 INFO @ Sun, 21 Jun 2020 17:57:16: 3000000 INFO @ Sun, 21 Jun 2020 17:57:18: 9000000 INFO @ Sun, 21 Jun 2020 17:57:20: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:57:20: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:57:20: #1 total tags in treatment: 9333338 INFO @ Sun, 21 Jun 2020 17:57:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:57:20: #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 17:57:20: #1 tags after filtering in treatment: 9333232 INFO @ Sun, 21 Jun 2020 17:57:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:57:20: #1 finished! INFO @ Sun, 21 Jun 2020 17:57:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:57:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:57:21: #2 number of paired peaks: 985 WARNING @ Sun, 21 Jun 2020 17:57:21: Fewer paired peaks (985) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 985 pairs to build model! INFO @ Sun, 21 Jun 2020 17:57:21: start model_add_line... INFO @ Sun, 21 Jun 2020 17:57:21: start X-correlation... INFO @ Sun, 21 Jun 2020 17:57:21: end of X-cor INFO @ Sun, 21 Jun 2020 17:57:21: #2 finished! INFO @ Sun, 21 Jun 2020 17:57:21: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 17:57:21: #2 alternative fragment length(s) may be 3,56,565,598 bps INFO @ Sun, 21 Jun 2020 17:57:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1794227/SRX1794227.05_model.r WARNING @ Sun, 21 Jun 2020 17:57:21: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:57:21: #2 You may need to consider one of the other alternative d(s): 3,56,565,598 WARNING @ Sun, 21 Jun 2020 17:57:21: #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 17:57:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:57:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:57:22: 4000000 INFO @ Sun, 21 Jun 2020 17:57:27: 5000000 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 17:57:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1794227/SRX1794227.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1794227/SRX1794227.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1794227/SRX1794227.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1794227/SRX1794227.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 17:57:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:57:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:57:33: 6000000 INFO @ Sun, 21 Jun 2020 17:57:35: 1000000 INFO @ Sun, 21 Jun 2020 17:57:38: 7000000 INFO @ Sun, 21 Jun 2020 17:57:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:57:40: 2000000 INFO @ Sun, 21 Jun 2020 17:57:43: 8000000 INFO @ Sun, 21 Jun 2020 17:57:45: 3000000 INFO @ Sun, 21 Jun 2020 17:57:49: 9000000 INFO @ Sun, 21 Jun 2020 17:57:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1794227/SRX1794227.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:57:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1794227/SRX1794227.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:57:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1794227/SRX1794227.05_summits.bed INFO @ Sun, 21 Jun 2020 17:57:49: Done! INFO @ Sun, 21 Jun 2020 17:57:50: 4000000 pass1 - making usageList (515 chroms): 2 millis pass2 - checking and writing primary data (2036 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:57:51: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:57:51: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:57:51: #1 total tags in treatment: 9333338 INFO @ Sun, 21 Jun 2020 17:57:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:57:51: #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 17:57:51: #1 tags after filtering in treatment: 9333232 INFO @ Sun, 21 Jun 2020 17:57:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:57:51: #1 finished! INFO @ Sun, 21 Jun 2020 17:57:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:57:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:57:52: #2 number of paired peaks: 985 WARNING @ Sun, 21 Jun 2020 17:57:52: Fewer paired peaks (985) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 985 pairs to build model! INFO @ Sun, 21 Jun 2020 17:57:52: start model_add_line... INFO @ Sun, 21 Jun 2020 17:57:52: start X-correlation... INFO @ Sun, 21 Jun 2020 17:57:52: end of X-cor INFO @ Sun, 21 Jun 2020 17:57:52: #2 finished! INFO @ Sun, 21 Jun 2020 17:57:52: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 17:57:52: #2 alternative fragment length(s) may be 3,56,565,598 bps INFO @ Sun, 21 Jun 2020 17:57:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1794227/SRX1794227.10_model.r WARNING @ Sun, 21 Jun 2020 17:57:52: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:57:52: #2 You may need to consider one of the other alternative d(s): 3,56,565,598 WARNING @ Sun, 21 Jun 2020 17:57:52: #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 17:57:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:57:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:57:54: 5000000 INFO @ Sun, 21 Jun 2020 17:57:59: 6000000 INFO @ Sun, 21 Jun 2020 17:58:04: 7000000 INFO @ Sun, 21 Jun 2020 17:58:09: 8000000 INFO @ Sun, 21 Jun 2020 17:58:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:58:13: 9000000 INFO @ Sun, 21 Jun 2020 17:58:15: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:58:15: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:58:15: #1 total tags in treatment: 9333338 INFO @ Sun, 21 Jun 2020 17:58:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:58:15: #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 17:58:16: #1 tags after filtering in treatment: 9333232 INFO @ Sun, 21 Jun 2020 17:58:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:58:16: #1 finished! INFO @ Sun, 21 Jun 2020 17:58:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:58:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:58:16: #2 number of paired peaks: 985 WARNING @ Sun, 21 Jun 2020 17:58:16: Fewer paired peaks (985) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 985 pairs to build model! INFO @ Sun, 21 Jun 2020 17:58:16: start model_add_line... INFO @ Sun, 21 Jun 2020 17:58:16: start X-correlation... INFO @ Sun, 21 Jun 2020 17:58:16: end of X-cor INFO @ Sun, 21 Jun 2020 17:58:16: #2 finished! INFO @ Sun, 21 Jun 2020 17:58:16: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 17:58:16: #2 alternative fragment length(s) may be 3,56,565,598 bps INFO @ Sun, 21 Jun 2020 17:58:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1794227/SRX1794227.20_model.r WARNING @ Sun, 21 Jun 2020 17:58:16: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:58:16: #2 You may need to consider one of the other alternative d(s): 3,56,565,598 WARNING @ Sun, 21 Jun 2020 17:58:16: #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 17:58:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:58:16: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:58:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1794227/SRX1794227.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:58:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1794227/SRX1794227.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:58:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1794227/SRX1794227.10_summits.bed INFO @ Sun, 21 Jun 2020 17:58:20: Done! pass1 - making usageList (346 chroms): 1 millis pass2 - checking and writing primary data (926 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:58:36: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:58:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1794227/SRX1794227.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:58:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1794227/SRX1794227.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:58:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1794227/SRX1794227.20_summits.bed INFO @ Sun, 21 Jun 2020 17:58:45: Done! pass1 - making usageList (142 chroms): 1 millis pass2 - checking and writing primary data (329 records, 4 fields): 5 millis CompletedMACS2peakCalling