Job ID = 6498368 SRX = SRX495195 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:47:25 prefetch.2.10.7: 1) Downloading 'SRR1198700'... 2020-06-25T23:47:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:49:11 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:49:11 prefetch.2.10.7: 1) 'SRR1198700' was downloaded successfully Read 19141145 spots for SRR1198700/SRR1198700.sra Written 19141145 spots for SRR1198700/SRR1198700.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: 00:04:20 19141145 reads; of these: 19141145 (100.00%) were unpaired; of these: 2467833 (12.89%) aligned 0 times 14881923 (77.75%) aligned exactly 1 time 1791389 (9.36%) aligned >1 times 87.11% overall alignment rate Time searching: 00:04:20 Overall time: 00:04:20 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] 2976296 / 16673312 = 0.1785 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 08:58:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495195/SRX495195.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495195/SRX495195.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495195/SRX495195.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495195/SRX495195.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 08:58:50: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:58:50: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:58:56: 1000000 INFO @ Fri, 26 Jun 2020 08:59:02: 2000000 INFO @ Fri, 26 Jun 2020 08:59:09: 3000000 INFO @ Fri, 26 Jun 2020 08:59:15: 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 08:59:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495195/SRX495195.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495195/SRX495195.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495195/SRX495195.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495195/SRX495195.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 08:59:20: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:59:20: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:59:21: 5000000 INFO @ Fri, 26 Jun 2020 08:59:27: 1000000 INFO @ Fri, 26 Jun 2020 08:59:28: 6000000 INFO @ Fri, 26 Jun 2020 08:59:34: 2000000 INFO @ Fri, 26 Jun 2020 08:59:34: 7000000 INFO @ Fri, 26 Jun 2020 08:59:41: 3000000 INFO @ Fri, 26 Jun 2020 08:59:41: 8000000 INFO @ Fri, 26 Jun 2020 08:59:48: 4000000 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 08:59:48: 9000000 INFO @ Fri, 26 Jun 2020 08:59:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX495195/SRX495195.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX495195/SRX495195.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX495195/SRX495195.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX495195/SRX495195.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 08:59:50: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:59:50: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:59:55: 5000000 INFO @ Fri, 26 Jun 2020 08:59:55: 10000000 INFO @ Fri, 26 Jun 2020 08:59:57: 1000000 INFO @ Fri, 26 Jun 2020 09:00:02: 6000000 INFO @ Fri, 26 Jun 2020 09:00:02: 11000000 INFO @ Fri, 26 Jun 2020 09:00:04: 2000000 INFO @ Fri, 26 Jun 2020 09:00:09: 7000000 INFO @ Fri, 26 Jun 2020 09:00:09: 12000000 INFO @ Fri, 26 Jun 2020 09:00:11: 3000000 INFO @ Fri, 26 Jun 2020 09:00:16: 8000000 INFO @ Fri, 26 Jun 2020 09:00:17: 13000000 INFO @ Fri, 26 Jun 2020 09:00:18: 4000000 INFO @ Fri, 26 Jun 2020 09:00:21: #1 tag size is determined as 44 bps INFO @ Fri, 26 Jun 2020 09:00:21: #1 tag size = 44 INFO @ Fri, 26 Jun 2020 09:00:21: #1 total tags in treatment: 13697016 INFO @ Fri, 26 Jun 2020 09:00:21: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:00:21: #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 09:00:22: #1 tags after filtering in treatment: 13697016 INFO @ Fri, 26 Jun 2020 09:00:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:00:22: #1 finished! INFO @ Fri, 26 Jun 2020 09:00:22: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:00:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:00:23: #2 number of paired peaks: 108 WARNING @ Fri, 26 Jun 2020 09:00:23: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Fri, 26 Jun 2020 09:00:23: start model_add_line... INFO @ Fri, 26 Jun 2020 09:00:23: start X-correlation... INFO @ Fri, 26 Jun 2020 09:00:23: end of X-cor INFO @ Fri, 26 Jun 2020 09:00:23: #2 finished! INFO @ Fri, 26 Jun 2020 09:00:23: #2 predicted fragment length is 9 bps INFO @ Fri, 26 Jun 2020 09:00:23: #2 alternative fragment length(s) may be 9,37,66 bps INFO @ Fri, 26 Jun 2020 09:00:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495195/SRX495195.05_model.r WARNING @ Fri, 26 Jun 2020 09:00:23: #2 Since the d (9) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:00:23: #2 You may need to consider one of the other alternative d(s): 9,37,66 WARNING @ Fri, 26 Jun 2020 09:00:23: #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 09:00:23: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:00:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:00:23: 9000000 INFO @ Fri, 26 Jun 2020 09:00:25: 5000000 INFO @ Fri, 26 Jun 2020 09:00:30: 10000000 INFO @ Fri, 26 Jun 2020 09:00:32: 6000000 INFO @ Fri, 26 Jun 2020 09:00:38: 11000000 INFO @ Fri, 26 Jun 2020 09:00:39: 7000000 INFO @ Fri, 26 Jun 2020 09:00:45: 12000000 INFO @ Fri, 26 Jun 2020 09:00:46: 8000000 INFO @ Fri, 26 Jun 2020 09:00:52: 13000000 INFO @ Fri, 26 Jun 2020 09:00:52: 9000000 INFO @ Fri, 26 Jun 2020 09:00:53: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:00:57: #1 tag size is determined as 44 bps INFO @ Fri, 26 Jun 2020 09:00:57: #1 tag size = 44 INFO @ Fri, 26 Jun 2020 09:00:57: #1 total tags in treatment: 13697016 INFO @ Fri, 26 Jun 2020 09:00:57: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:00:57: #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 09:00:57: #1 tags after filtering in treatment: 13697016 INFO @ Fri, 26 Jun 2020 09:00:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:00:57: #1 finished! INFO @ Fri, 26 Jun 2020 09:00:57: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:00:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:00:58: #2 number of paired peaks: 108 WARNING @ Fri, 26 Jun 2020 09:00:58: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Fri, 26 Jun 2020 09:00:58: start model_add_line... INFO @ Fri, 26 Jun 2020 09:00:59: start X-correlation... INFO @ Fri, 26 Jun 2020 09:00:59: end of X-cor INFO @ Fri, 26 Jun 2020 09:00:59: #2 finished! INFO @ Fri, 26 Jun 2020 09:00:59: #2 predicted fragment length is 9 bps INFO @ Fri, 26 Jun 2020 09:00:59: #2 alternative fragment length(s) may be 9,37,66 bps INFO @ Fri, 26 Jun 2020 09:00:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495195/SRX495195.10_model.r WARNING @ Fri, 26 Jun 2020 09:00:59: #2 Since the d (9) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:00:59: #2 You may need to consider one of the other alternative d(s): 9,37,66 WARNING @ Fri, 26 Jun 2020 09:00:59: #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 09:00:59: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:00:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:00:59: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:01:05: 11000000 INFO @ Fri, 26 Jun 2020 09:01:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495195/SRX495195.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:01:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495195/SRX495195.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:01:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495195/SRX495195.05_summits.bed INFO @ Fri, 26 Jun 2020 09:01:08: Done! pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:01:12: 12000000 INFO @ Fri, 26 Jun 2020 09:01:18: 13000000 INFO @ Fri, 26 Jun 2020 09:01:23: #1 tag size is determined as 44 bps INFO @ Fri, 26 Jun 2020 09:01:23: #1 tag size = 44 INFO @ Fri, 26 Jun 2020 09:01:23: #1 total tags in treatment: 13697016 INFO @ Fri, 26 Jun 2020 09:01:23: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:01:23: #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 09:01:23: #1 tags after filtering in treatment: 13697016 INFO @ Fri, 26 Jun 2020 09:01:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:01:23: #1 finished! INFO @ Fri, 26 Jun 2020 09:01:23: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:01:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:01:24: #2 number of paired peaks: 108 WARNING @ Fri, 26 Jun 2020 09:01:24: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Fri, 26 Jun 2020 09:01:24: start model_add_line... INFO @ Fri, 26 Jun 2020 09:01:24: start X-correlation... INFO @ Fri, 26 Jun 2020 09:01:24: end of X-cor INFO @ Fri, 26 Jun 2020 09:01:24: #2 finished! INFO @ Fri, 26 Jun 2020 09:01:24: #2 predicted fragment length is 9 bps INFO @ Fri, 26 Jun 2020 09:01:24: #2 alternative fragment length(s) may be 9,37,66 bps INFO @ Fri, 26 Jun 2020 09:01:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX495195/SRX495195.20_model.r WARNING @ Fri, 26 Jun 2020 09:01:24: #2 Since the d (9) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:01:24: #2 You may need to consider one of the other alternative d(s): 9,37,66 WARNING @ Fri, 26 Jun 2020 09:01:24: #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 09:01:24: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:01:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:01:30: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:01:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495195/SRX495195.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:01:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495195/SRX495195.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:01:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495195/SRX495195.10_summits.bed INFO @ Fri, 26 Jun 2020 09:01:45: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:01:55: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:02:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX495195/SRX495195.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:02:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX495195/SRX495195.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:02:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX495195/SRX495195.20_summits.bed INFO @ Fri, 26 Jun 2020 09:02:09: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling