Job ID = 6457928 SRX = SRX4923175 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:01:50 prefetch.2.10.7: 1) Downloading 'SRR8096325'... 2020-06-21T12:01:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:03:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:03:43 prefetch.2.10.7: 1) 'SRR8096325' was downloaded successfully 2020-06-21T12:03:43 prefetch.2.10.7: 'SRR8096325' has 0 unresolved dependencies Read 33733286 spots for SRR8096325/SRR8096325.sra Written 33733286 spots for SRR8096325/SRR8096325.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: 00:07:41 33733286 reads; of these: 33733286 (100.00%) were unpaired; of these: 2220691 (6.58%) aligned 0 times 26432963 (78.36%) aligned exactly 1 time 5079632 (15.06%) aligned >1 times 93.42% overall alignment rate Time searching: 00:07:41 Overall time: 00:07:41 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 16 files... [bam_rmdupse_core] 8248595 / 31512595 = 0.2618 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 21:18:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923175/SRX4923175.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923175/SRX4923175.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923175/SRX4923175.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923175/SRX4923175.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 21:18:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:18:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:18:21: 1000000 INFO @ Sun, 21 Jun 2020 21:18:25: 2000000 INFO @ Sun, 21 Jun 2020 21:18:30: 3000000 INFO @ Sun, 21 Jun 2020 21:18:35: 4000000 INFO @ Sun, 21 Jun 2020 21:18:40: 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 21:18:45: 6000000 INFO @ Sun, 21 Jun 2020 21:18:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923175/SRX4923175.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923175/SRX4923175.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923175/SRX4923175.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923175/SRX4923175.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 21:18:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:18:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:18:50: 7000000 INFO @ Sun, 21 Jun 2020 21:18:51: 1000000 INFO @ Sun, 21 Jun 2020 21:18:55: 8000000 INFO @ Sun, 21 Jun 2020 21:18:56: 2000000 INFO @ Sun, 21 Jun 2020 21:19:00: 9000000 INFO @ Sun, 21 Jun 2020 21:19:02: 3000000 INFO @ Sun, 21 Jun 2020 21:19:05: 10000000 INFO @ Sun, 21 Jun 2020 21:19:07: 4000000 INFO @ Sun, 21 Jun 2020 21:19:10: 11000000 INFO @ Sun, 21 Jun 2020 21:19:12: 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 21:19:16: 12000000 INFO @ Sun, 21 Jun 2020 21:19:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4923175/SRX4923175.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4923175/SRX4923175.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4923175/SRX4923175.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4923175/SRX4923175.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 21:19:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:19:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:19:17: 6000000 INFO @ Sun, 21 Jun 2020 21:19:21: 13000000 INFO @ Sun, 21 Jun 2020 21:19:21: 1000000 INFO @ Sun, 21 Jun 2020 21:19:22: 7000000 INFO @ Sun, 21 Jun 2020 21:19:26: 14000000 INFO @ Sun, 21 Jun 2020 21:19:27: 2000000 INFO @ Sun, 21 Jun 2020 21:19:27: 8000000 INFO @ Sun, 21 Jun 2020 21:19:32: 15000000 INFO @ Sun, 21 Jun 2020 21:19:33: 9000000 INFO @ Sun, 21 Jun 2020 21:19:33: 3000000 INFO @ Sun, 21 Jun 2020 21:19:37: 16000000 INFO @ Sun, 21 Jun 2020 21:19:38: 10000000 INFO @ Sun, 21 Jun 2020 21:19:39: 4000000 INFO @ Sun, 21 Jun 2020 21:19:43: 17000000 INFO @ Sun, 21 Jun 2020 21:19:43: 11000000 INFO @ Sun, 21 Jun 2020 21:19:45: 5000000 INFO @ Sun, 21 Jun 2020 21:19:48: 18000000 INFO @ Sun, 21 Jun 2020 21:19:48: 12000000 INFO @ Sun, 21 Jun 2020 21:19:50: 6000000 INFO @ Sun, 21 Jun 2020 21:19:53: 13000000 INFO @ Sun, 21 Jun 2020 21:19:54: 19000000 INFO @ Sun, 21 Jun 2020 21:19:56: 7000000 INFO @ Sun, 21 Jun 2020 21:19:59: 14000000 INFO @ Sun, 21 Jun 2020 21:19:59: 20000000 INFO @ Sun, 21 Jun 2020 21:20:02: 8000000 INFO @ Sun, 21 Jun 2020 21:20:04: 15000000 INFO @ Sun, 21 Jun 2020 21:20:05: 21000000 INFO @ Sun, 21 Jun 2020 21:20:07: 9000000 INFO @ Sun, 21 Jun 2020 21:20:09: 16000000 INFO @ Sun, 21 Jun 2020 21:20:10: 22000000 INFO @ Sun, 21 Jun 2020 21:20:13: 10000000 INFO @ Sun, 21 Jun 2020 21:20:14: 17000000 INFO @ Sun, 21 Jun 2020 21:20:16: 23000000 INFO @ Sun, 21 Jun 2020 21:20:17: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:20:17: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:20:17: #1 total tags in treatment: 23264000 INFO @ Sun, 21 Jun 2020 21:20:17: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:20:17: #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 21:20:18: #1 tags after filtering in treatment: 23263919 INFO @ Sun, 21 Jun 2020 21:20:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:20:18: #1 finished! INFO @ Sun, 21 Jun 2020 21:20:18: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:20:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:20:19: 11000000 INFO @ Sun, 21 Jun 2020 21:20:20: #2 number of paired peaks: 187 WARNING @ Sun, 21 Jun 2020 21:20:20: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Sun, 21 Jun 2020 21:20:20: start model_add_line... INFO @ Sun, 21 Jun 2020 21:20:20: 18000000 INFO @ Sun, 21 Jun 2020 21:20:20: start X-correlation... INFO @ Sun, 21 Jun 2020 21:20:20: end of X-cor INFO @ Sun, 21 Jun 2020 21:20:20: #2 finished! INFO @ Sun, 21 Jun 2020 21:20:20: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 21:20:20: #2 alternative fragment length(s) may be 1,31,48,531,546 bps INFO @ Sun, 21 Jun 2020 21:20:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923175/SRX4923175.05_model.r WARNING @ Sun, 21 Jun 2020 21:20:20: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:20:20: #2 You may need to consider one of the other alternative d(s): 1,31,48,531,546 WARNING @ Sun, 21 Jun 2020 21:20:20: #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 21:20:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:20:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:20:25: 12000000 INFO @ Sun, 21 Jun 2020 21:20:25: 19000000 INFO @ Sun, 21 Jun 2020 21:20:30: 13000000 INFO @ Sun, 21 Jun 2020 21:20:30: 20000000 INFO @ Sun, 21 Jun 2020 21:20:36: 21000000 INFO @ Sun, 21 Jun 2020 21:20:36: 14000000 INFO @ Sun, 21 Jun 2020 21:20:41: 22000000 INFO @ Sun, 21 Jun 2020 21:20:42: 15000000 INFO @ Sun, 21 Jun 2020 21:20:46: 23000000 INFO @ Sun, 21 Jun 2020 21:20:48: 16000000 INFO @ Sun, 21 Jun 2020 21:20:48: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:20:48: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:20:48: #1 total tags in treatment: 23264000 INFO @ Sun, 21 Jun 2020 21:20:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:20:48: #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 21:20:49: #1 tags after filtering in treatment: 23263919 INFO @ Sun, 21 Jun 2020 21:20:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:20:49: #1 finished! INFO @ Sun, 21 Jun 2020 21:20:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:20:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:20:50: #2 number of paired peaks: 187 WARNING @ Sun, 21 Jun 2020 21:20:50: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Sun, 21 Jun 2020 21:20:50: start model_add_line... INFO @ Sun, 21 Jun 2020 21:20:50: start X-correlation... INFO @ Sun, 21 Jun 2020 21:20:50: end of X-cor INFO @ Sun, 21 Jun 2020 21:20:50: #2 finished! INFO @ Sun, 21 Jun 2020 21:20:50: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 21:20:50: #2 alternative fragment length(s) may be 1,31,48,531,546 bps INFO @ Sun, 21 Jun 2020 21:20:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923175/SRX4923175.10_model.r WARNING @ Sun, 21 Jun 2020 21:20:50: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:20:50: #2 You may need to consider one of the other alternative d(s): 1,31,48,531,546 WARNING @ Sun, 21 Jun 2020 21:20:50: #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 21:20:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:20:50: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:20:54: 17000000 INFO @ Sun, 21 Jun 2020 21:20:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:21:00: 18000000 INFO @ Sun, 21 Jun 2020 21:21:06: 19000000 INFO @ Sun, 21 Jun 2020 21:21:11: 20000000 INFO @ Sun, 21 Jun 2020 21:21:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923175/SRX4923175.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:21:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923175/SRX4923175.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:21:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923175/SRX4923175.05_summits.bed INFO @ Sun, 21 Jun 2020 21:21:16: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:21:17: 21000000 INFO @ Sun, 21 Jun 2020 21:21:22: 22000000 INFO @ Sun, 21 Jun 2020 21:21:28: 23000000 INFO @ Sun, 21 Jun 2020 21:21:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:21:30: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:21:30: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:21:30: #1 total tags in treatment: 23264000 INFO @ Sun, 21 Jun 2020 21:21:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:21:30: #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 21:21:30: #1 tags after filtering in treatment: 23263919 INFO @ Sun, 21 Jun 2020 21:21:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:21:30: #1 finished! INFO @ Sun, 21 Jun 2020 21:21:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:21:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:21:32: #2 number of paired peaks: 187 WARNING @ Sun, 21 Jun 2020 21:21:32: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Sun, 21 Jun 2020 21:21:32: start model_add_line... INFO @ Sun, 21 Jun 2020 21:21:32: start X-correlation... INFO @ Sun, 21 Jun 2020 21:21:32: end of X-cor INFO @ Sun, 21 Jun 2020 21:21:32: #2 finished! INFO @ Sun, 21 Jun 2020 21:21:32: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 21:21:32: #2 alternative fragment length(s) may be 1,31,48,531,546 bps INFO @ Sun, 21 Jun 2020 21:21:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4923175/SRX4923175.20_model.r WARNING @ Sun, 21 Jun 2020 21:21:32: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:21:32: #2 You may need to consider one of the other alternative d(s): 1,31,48,531,546 WARNING @ Sun, 21 Jun 2020 21:21:32: #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 21:21:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:21:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:21:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923175/SRX4923175.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:21:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923175/SRX4923175.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:21:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923175/SRX4923175.10_summits.bed INFO @ Sun, 21 Jun 2020 21:21:46: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:22:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:22:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4923175/SRX4923175.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:22:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4923175/SRX4923175.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:22:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4923175/SRX4923175.20_summits.bed INFO @ Sun, 21 Jun 2020 21:22:30: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling