Job ID = 6456364 SRX = SRX3380808 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:51:31 prefetch.2.10.7: 1) Downloading 'SRR6278171'... 2020-06-21T10:51:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:55:25 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:55:26 prefetch.2.10.7: 'SRR6278171' is valid 2020-06-21T10:55:26 prefetch.2.10.7: 1) 'SRR6278171' was downloaded successfully Read 19702923 spots for SRR6278171/SRR6278171.sra Written 19702923 spots for SRR6278171/SRR6278171.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: 00:05:00 19702923 reads; of these: 19702923 (100.00%) were unpaired; of these: 1877727 (9.53%) aligned 0 times 13971637 (70.91%) aligned exactly 1 time 3853559 (19.56%) aligned >1 times 90.47% overall alignment rate Time searching: 00:05:00 Overall time: 00:05:00 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] 3227219 / 17825196 = 0.1810 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 20:05:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380808/SRX3380808.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380808/SRX3380808.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380808/SRX3380808.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380808/SRX3380808.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 20:05:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:05:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:05:34: 1000000 INFO @ Sun, 21 Jun 2020 20:05:40: 2000000 INFO @ Sun, 21 Jun 2020 20:05:45: 3000000 INFO @ Sun, 21 Jun 2020 20:05:50: 4000000 INFO @ Sun, 21 Jun 2020 20:05:56: 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 20:05:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380808/SRX3380808.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380808/SRX3380808.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380808/SRX3380808.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380808/SRX3380808.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 20:05:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:05:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:06:01: 6000000 INFO @ Sun, 21 Jun 2020 20:06:05: 1000000 INFO @ Sun, 21 Jun 2020 20:06:07: 7000000 INFO @ Sun, 21 Jun 2020 20:06:11: 2000000 INFO @ Sun, 21 Jun 2020 20:06:13: 8000000 INFO @ Sun, 21 Jun 2020 20:06:16: 3000000 INFO @ Sun, 21 Jun 2020 20:06:18: 9000000 INFO @ Sun, 21 Jun 2020 20:06:22: 4000000 INFO @ Sun, 21 Jun 2020 20:06:24: 10000000 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 20:06:28: 5000000 INFO @ Sun, 21 Jun 2020 20:06:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380808/SRX3380808.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380808/SRX3380808.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380808/SRX3380808.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380808/SRX3380808.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 20:06:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:06:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:06:30: 11000000 INFO @ Sun, 21 Jun 2020 20:06:34: 6000000 INFO @ Sun, 21 Jun 2020 20:06:35: 1000000 INFO @ Sun, 21 Jun 2020 20:06:36: 12000000 INFO @ Sun, 21 Jun 2020 20:06:40: 7000000 INFO @ Sun, 21 Jun 2020 20:06:41: 2000000 INFO @ Sun, 21 Jun 2020 20:06:42: 13000000 INFO @ Sun, 21 Jun 2020 20:06:45: 8000000 INFO @ Sun, 21 Jun 2020 20:06:47: 3000000 INFO @ Sun, 21 Jun 2020 20:06:48: 14000000 INFO @ Sun, 21 Jun 2020 20:06:51: 9000000 INFO @ Sun, 21 Jun 2020 20:06:51: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:06:51: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:06:51: #1 total tags in treatment: 14597977 INFO @ Sun, 21 Jun 2020 20:06:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:06:51: #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 20:06:52: #1 tags after filtering in treatment: 14597974 INFO @ Sun, 21 Jun 2020 20:06:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:06:52: #1 finished! INFO @ Sun, 21 Jun 2020 20:06:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:06:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:06:52: 4000000 INFO @ Sun, 21 Jun 2020 20:06:53: #2 number of paired peaks: 273 WARNING @ Sun, 21 Jun 2020 20:06:53: Fewer paired peaks (273) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 273 pairs to build model! INFO @ Sun, 21 Jun 2020 20:06:53: start model_add_line... INFO @ Sun, 21 Jun 2020 20:06:53: start X-correlation... INFO @ Sun, 21 Jun 2020 20:06:53: end of X-cor INFO @ Sun, 21 Jun 2020 20:06:53: #2 finished! INFO @ Sun, 21 Jun 2020 20:06:53: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 20:06:53: #2 alternative fragment length(s) may be 3,45 bps INFO @ Sun, 21 Jun 2020 20:06:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380808/SRX3380808.05_model.r WARNING @ Sun, 21 Jun 2020 20:06:53: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:06:53: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Sun, 21 Jun 2020 20:06:53: #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 20:06:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:06:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:06:57: 10000000 INFO @ Sun, 21 Jun 2020 20:06:58: 5000000 INFO @ Sun, 21 Jun 2020 20:07:03: 11000000 INFO @ Sun, 21 Jun 2020 20:07:04: 6000000 INFO @ Sun, 21 Jun 2020 20:07:09: 12000000 INFO @ Sun, 21 Jun 2020 20:07:10: 7000000 INFO @ Sun, 21 Jun 2020 20:07:15: 13000000 INFO @ Sun, 21 Jun 2020 20:07:16: 8000000 INFO @ Sun, 21 Jun 2020 20:07:20: 14000000 INFO @ Sun, 21 Jun 2020 20:07:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:07:22: 9000000 INFO @ Sun, 21 Jun 2020 20:07:24: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:07:24: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:07:24: #1 total tags in treatment: 14597977 INFO @ Sun, 21 Jun 2020 20:07:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:07:24: #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 20:07:25: #1 tags after filtering in treatment: 14597974 INFO @ Sun, 21 Jun 2020 20:07:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:07:25: #1 finished! INFO @ Sun, 21 Jun 2020 20:07:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:07:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:07:26: #2 number of paired peaks: 273 WARNING @ Sun, 21 Jun 2020 20:07:26: Fewer paired peaks (273) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 273 pairs to build model! INFO @ Sun, 21 Jun 2020 20:07:26: start model_add_line... INFO @ Sun, 21 Jun 2020 20:07:26: start X-correlation... INFO @ Sun, 21 Jun 2020 20:07:26: end of X-cor INFO @ Sun, 21 Jun 2020 20:07:26: #2 finished! INFO @ Sun, 21 Jun 2020 20:07:26: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 20:07:26: #2 alternative fragment length(s) may be 3,45 bps INFO @ Sun, 21 Jun 2020 20:07:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380808/SRX3380808.10_model.r WARNING @ Sun, 21 Jun 2020 20:07:26: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:07:26: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Sun, 21 Jun 2020 20:07:26: #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 20:07:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:07:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:07:27: 10000000 INFO @ Sun, 21 Jun 2020 20:07:33: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:07:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380808/SRX3380808.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:07:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380808/SRX3380808.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:07:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380808/SRX3380808.05_summits.bed INFO @ Sun, 21 Jun 2020 20:07:34: Done! pass1 - making usageList (505 chroms): 2 millis pass2 - checking and writing primary data (2760 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:07:39: 12000000 INFO @ Sun, 21 Jun 2020 20:07:44: 13000000 INFO @ Sun, 21 Jun 2020 20:07:50: 14000000 INFO @ Sun, 21 Jun 2020 20:07:53: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:07:53: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:07:53: #1 total tags in treatment: 14597977 INFO @ Sun, 21 Jun 2020 20:07:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:07:53: #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 20:07:54: #1 tags after filtering in treatment: 14597974 INFO @ Sun, 21 Jun 2020 20:07:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:07:54: #1 finished! INFO @ Sun, 21 Jun 2020 20:07:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:07:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:07:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:07:55: #2 number of paired peaks: 273 WARNING @ Sun, 21 Jun 2020 20:07:55: Fewer paired peaks (273) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 273 pairs to build model! INFO @ Sun, 21 Jun 2020 20:07:55: start model_add_line... INFO @ Sun, 21 Jun 2020 20:07:55: start X-correlation... INFO @ Sun, 21 Jun 2020 20:07:55: end of X-cor INFO @ Sun, 21 Jun 2020 20:07:55: #2 finished! INFO @ Sun, 21 Jun 2020 20:07:55: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 20:07:55: #2 alternative fragment length(s) may be 3,45 bps INFO @ Sun, 21 Jun 2020 20:07:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380808/SRX3380808.20_model.r WARNING @ Sun, 21 Jun 2020 20:07:55: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:07:55: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Sun, 21 Jun 2020 20:07:55: #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 20:07:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:07:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:08:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380808/SRX3380808.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:08:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380808/SRX3380808.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:08:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380808/SRX3380808.10_summits.bed INFO @ Sun, 21 Jun 2020 20:08:08: Done! pass1 - making usageList (404 chroms): 2 millis pass2 - checking and writing primary data (1301 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:08:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:08:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380808/SRX3380808.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:08:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380808/SRX3380808.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:08:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380808/SRX3380808.20_summits.bed INFO @ Sun, 21 Jun 2020 20:08:37: Done! pass1 - making usageList (170 chroms): 1 millis pass2 - checking and writing primary data (303 records, 4 fields): 6 millis CompletedMACS2peakCalling