Job ID = 6498298 SRX = SRX467109 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:13:18 prefetch.2.10.7: 1) Downloading 'SRR1164533'... 2020-06-25T23:13:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:14:27 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:14:28 prefetch.2.10.7: 'SRR1164533' is valid 2020-06-25T23:14:28 prefetch.2.10.7: 1) 'SRR1164533' was downloaded successfully Read 11858540 spots for SRR1164533/SRR1164533.sra Written 11858540 spots for SRR1164533/SRR1164533.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: 00:04:05 11858540 reads; of these: 11858540 (100.00%) were unpaired; of these: 623070 (5.25%) aligned 0 times 7872619 (66.39%) aligned exactly 1 time 3362851 (28.36%) aligned >1 times 94.75% overall alignment rate Time searching: 00:04:05 Overall time: 00:04:05 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1192253 / 11235470 = 0.1061 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 @ Fri, 26 Jun 2020 08:23:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467109/SRX467109.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467109/SRX467109.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467109/SRX467109.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467109/SRX467109.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 @ Fri, 26 Jun 2020 08:23:14: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:23:14: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:23:20: 1000000 INFO @ Fri, 26 Jun 2020 08:23:26: 2000000 INFO @ Fri, 26 Jun 2020 08:23:33: 3000000 INFO @ Fri, 26 Jun 2020 08:23:39: 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 @ Fri, 26 Jun 2020 08:23:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467109/SRX467109.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467109/SRX467109.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467109/SRX467109.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467109/SRX467109.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 @ Fri, 26 Jun 2020 08:23:44: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:23:44: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:23:45: 5000000 INFO @ Fri, 26 Jun 2020 08:23:51: 1000000 INFO @ Fri, 26 Jun 2020 08:23:51: 6000000 INFO @ Fri, 26 Jun 2020 08:23:57: 2000000 INFO @ Fri, 26 Jun 2020 08:23:57: 7000000 INFO @ Fri, 26 Jun 2020 08:24:04: 3000000 INFO @ Fri, 26 Jun 2020 08:24:04: 8000000 INFO @ Fri, 26 Jun 2020 08:24:10: 4000000 INFO @ Fri, 26 Jun 2020 08:24:11: 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 @ Fri, 26 Jun 2020 08:24:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467109/SRX467109.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467109/SRX467109.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467109/SRX467109.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467109/SRX467109.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 @ Fri, 26 Jun 2020 08:24:14: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:24:14: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:24:17: 5000000 INFO @ Fri, 26 Jun 2020 08:24:17: 10000000 INFO @ Fri, 26 Jun 2020 08:24:18: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:24:18: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:24:18: #1 total tags in treatment: 10043217 INFO @ Fri, 26 Jun 2020 08:24:18: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:24:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:24:18: #1 tags after filtering in treatment: 10043217 INFO @ Fri, 26 Jun 2020 08:24:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:24:18: #1 finished! INFO @ Fri, 26 Jun 2020 08:24:18: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:24:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:24:19: #2 number of paired peaks: 236 WARNING @ Fri, 26 Jun 2020 08:24:19: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Fri, 26 Jun 2020 08:24:19: start model_add_line... INFO @ Fri, 26 Jun 2020 08:24:19: start X-correlation... INFO @ Fri, 26 Jun 2020 08:24:19: end of X-cor INFO @ Fri, 26 Jun 2020 08:24:19: #2 finished! INFO @ Fri, 26 Jun 2020 08:24:19: #2 predicted fragment length is 58 bps INFO @ Fri, 26 Jun 2020 08:24:19: #2 alternative fragment length(s) may be 58 bps INFO @ Fri, 26 Jun 2020 08:24:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467109/SRX467109.05_model.r WARNING @ Fri, 26 Jun 2020 08:24:19: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:24:19: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Fri, 26 Jun 2020 08:24:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:24:19: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:24:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:24:21: 1000000 INFO @ Fri, 26 Jun 2020 08:24:23: 6000000 INFO @ Fri, 26 Jun 2020 08:24:26: 2000000 INFO @ Fri, 26 Jun 2020 08:24:29: 7000000 INFO @ Fri, 26 Jun 2020 08:24:32: 3000000 INFO @ Fri, 26 Jun 2020 08:24:36: 8000000 INFO @ Fri, 26 Jun 2020 08:24:37: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:24:38: 4000000 INFO @ Fri, 26 Jun 2020 08:24:42: 9000000 INFO @ Fri, 26 Jun 2020 08:24:44: 5000000 INFO @ Fri, 26 Jun 2020 08:24:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467109/SRX467109.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:24:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467109/SRX467109.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:24:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467109/SRX467109.05_summits.bed INFO @ Fri, 26 Jun 2020 08:24:47: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4215 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:24:48: 10000000 INFO @ Fri, 26 Jun 2020 08:24:49: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:24:49: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:24:49: #1 total tags in treatment: 10043217 INFO @ Fri, 26 Jun 2020 08:24:49: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:24:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:24:49: #1 tags after filtering in treatment: 10043217 INFO @ Fri, 26 Jun 2020 08:24:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:24:49: #1 finished! INFO @ Fri, 26 Jun 2020 08:24:49: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:24:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:24:50: #2 number of paired peaks: 236 WARNING @ Fri, 26 Jun 2020 08:24:50: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Fri, 26 Jun 2020 08:24:50: start model_add_line... INFO @ Fri, 26 Jun 2020 08:24:50: start X-correlation... INFO @ Fri, 26 Jun 2020 08:24:50: end of X-cor INFO @ Fri, 26 Jun 2020 08:24:50: #2 finished! INFO @ Fri, 26 Jun 2020 08:24:50: #2 predicted fragment length is 58 bps INFO @ Fri, 26 Jun 2020 08:24:50: #2 alternative fragment length(s) may be 58 bps INFO @ Fri, 26 Jun 2020 08:24:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467109/SRX467109.10_model.r WARNING @ Fri, 26 Jun 2020 08:24:50: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:24:50: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Fri, 26 Jun 2020 08:24:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:24:50: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:24:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:24:50: 6000000 INFO @ Fri, 26 Jun 2020 08:24:56: 7000000 INFO @ Fri, 26 Jun 2020 08:25:01: 8000000 INFO @ Fri, 26 Jun 2020 08:25:07: 9000000 INFO @ Fri, 26 Jun 2020 08:25:08: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:25:13: 10000000 INFO @ Fri, 26 Jun 2020 08:25:13: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:25:13: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:25:13: #1 total tags in treatment: 10043217 INFO @ Fri, 26 Jun 2020 08:25:13: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:25:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:25:13: #1 tags after filtering in treatment: 10043217 INFO @ Fri, 26 Jun 2020 08:25:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:25:13: #1 finished! INFO @ Fri, 26 Jun 2020 08:25:13: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:25:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:25:14: #2 number of paired peaks: 236 WARNING @ Fri, 26 Jun 2020 08:25:14: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Fri, 26 Jun 2020 08:25:14: start model_add_line... INFO @ Fri, 26 Jun 2020 08:25:14: start X-correlation... INFO @ Fri, 26 Jun 2020 08:25:14: end of X-cor INFO @ Fri, 26 Jun 2020 08:25:14: #2 finished! INFO @ Fri, 26 Jun 2020 08:25:14: #2 predicted fragment length is 58 bps INFO @ Fri, 26 Jun 2020 08:25:14: #2 alternative fragment length(s) may be 58 bps INFO @ Fri, 26 Jun 2020 08:25:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467109/SRX467109.20_model.r WARNING @ Fri, 26 Jun 2020 08:25:14: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:25:14: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Fri, 26 Jun 2020 08:25:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:25:14: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:25:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:25:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467109/SRX467109.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:25:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467109/SRX467109.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:25:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467109/SRX467109.10_summits.bed INFO @ Fri, 26 Jun 2020 08:25:17: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2402 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:25:32: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:25:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467109/SRX467109.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:25:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467109/SRX467109.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:25:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467109/SRX467109.20_summits.bed INFO @ Fri, 26 Jun 2020 08:25:42: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1045 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。