Job ID = 6458058 SRX = SRX495188 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:17:34 prefetch.2.10.7: 1) Downloading 'SRR1198693'... 2020-06-21T12:17:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:19:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:19:23 prefetch.2.10.7: 'SRR1198693' is valid 2020-06-21T12:19:23 prefetch.2.10.7: 1) 'SRR1198693' was downloaded successfully Read 18603228 spots for SRR1198693/SRR1198693.sra Written 18603228 spots for SRR1198693/SRR1198693.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: 00:02:27 18603228 reads; of these: 18603228 (100.00%) were unpaired; of these: 11632287 (62.53%) aligned 0 times 5876864 (31.59%) aligned exactly 1 time 1094077 (5.88%) aligned >1 times 37.47% overall alignment rate Time searching: 00:02:27 Overall time: 00:02:27 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_rmdupse_core] 1689999 / 6970941 = 0.2424 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 21:24:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495188/SRX495188.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495188/SRX495188.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495188/SRX495188.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495188/SRX495188.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 21:24:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:24:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:24:56: 1000000 INFO @ Sun, 21 Jun 2020 21:25:03: 2000000 INFO @ Sun, 21 Jun 2020 21:25:09: 3000000 INFO @ Sun, 21 Jun 2020 21:25:15: 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 @ Sun, 21 Jun 2020 21:25:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495188/SRX495188.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495188/SRX495188.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495188/SRX495188.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495188/SRX495188.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 21:25:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:25:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:25:21: 5000000 INFO @ Sun, 21 Jun 2020 21:25:23: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 21:25:23: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 21:25:23: #1 total tags in treatment: 5280942 INFO @ Sun, 21 Jun 2020 21:25:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:25:23: #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 21:25:24: #1 tags after filtering in treatment: 5280878 INFO @ Sun, 21 Jun 2020 21:25:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:25:24: #1 finished! INFO @ Sun, 21 Jun 2020 21:25:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:25:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:25:24: #2 number of paired peaks: 345 WARNING @ Sun, 21 Jun 2020 21:25:24: Fewer paired peaks (345) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 345 pairs to build model! INFO @ Sun, 21 Jun 2020 21:25:24: start model_add_line... INFO @ Sun, 21 Jun 2020 21:25:24: start X-correlation... INFO @ Sun, 21 Jun 2020 21:25:24: end of X-cor INFO @ Sun, 21 Jun 2020 21:25:24: #2 finished! INFO @ Sun, 21 Jun 2020 21:25:24: #2 predicted fragment length is 11 bps INFO @ Sun, 21 Jun 2020 21:25:24: #2 alternative fragment length(s) may be 11,43,70,522,539,591 bps INFO @ Sun, 21 Jun 2020 21:25:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495188/SRX495188.05_model.r WARNING @ Sun, 21 Jun 2020 21:25:24: #2 Since the d (11) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:25:24: #2 You may need to consider one of the other alternative d(s): 11,43,70,522,539,591 WARNING @ Sun, 21 Jun 2020 21:25:24: #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 21:25:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:25:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:25:27: 1000000 INFO @ Sun, 21 Jun 2020 21:25:33: 2000000 INFO @ Sun, 21 Jun 2020 21:25:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:25:39: 3000000 INFO @ Sun, 21 Jun 2020 21:25:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495188/SRX495188.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:25:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495188/SRX495188.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:25:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495188/SRX495188.05_summits.bed INFO @ Sun, 21 Jun 2020 21:25:43: Done! pass1 - making usageList (66 chroms): 1 millis pass2 - checking and writing primary data (110 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:25:46: 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 @ Sun, 21 Jun 2020 21:25:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495188/SRX495188.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495188/SRX495188.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495188/SRX495188.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495188/SRX495188.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 21:25:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:25:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:25:53: 5000000 INFO @ Sun, 21 Jun 2020 21:25:55: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 21:25:55: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 21:25:55: #1 total tags in treatment: 5280942 INFO @ Sun, 21 Jun 2020 21:25:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:25:55: #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 21:25:56: #1 tags after filtering in treatment: 5280878 INFO @ Sun, 21 Jun 2020 21:25:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:25:56: #1 finished! INFO @ Sun, 21 Jun 2020 21:25:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:25:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:25:56: #2 number of paired peaks: 345 WARNING @ Sun, 21 Jun 2020 21:25:56: Fewer paired peaks (345) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 345 pairs to build model! INFO @ Sun, 21 Jun 2020 21:25:56: start model_add_line... INFO @ Sun, 21 Jun 2020 21:25:56: start X-correlation... INFO @ Sun, 21 Jun 2020 21:25:56: end of X-cor INFO @ Sun, 21 Jun 2020 21:25:56: #2 finished! INFO @ Sun, 21 Jun 2020 21:25:56: #2 predicted fragment length is 11 bps INFO @ Sun, 21 Jun 2020 21:25:56: #2 alternative fragment length(s) may be 11,43,70,522,539,591 bps INFO @ Sun, 21 Jun 2020 21:25:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495188/SRX495188.10_model.r WARNING @ Sun, 21 Jun 2020 21:25:56: #2 Since the d (11) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:25:56: #2 You may need to consider one of the other alternative d(s): 11,43,70,522,539,591 WARNING @ Sun, 21 Jun 2020 21:25:56: #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 21:25:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:25:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:25:58: 1000000 INFO @ Sun, 21 Jun 2020 21:26:05: 2000000 INFO @ Sun, 21 Jun 2020 21:26:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:26:13: 3000000 INFO @ Sun, 21 Jun 2020 21:26:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495188/SRX495188.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:26:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495188/SRX495188.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:26:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495188/SRX495188.10_summits.bed INFO @ Sun, 21 Jun 2020 21:26:15: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (6 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:26:21: 4000000 INFO @ Sun, 21 Jun 2020 21:26:29: 5000000 INFO @ Sun, 21 Jun 2020 21:26:31: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 21:26:31: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 21:26:31: #1 total tags in treatment: 5280942 INFO @ Sun, 21 Jun 2020 21:26:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:26:31: #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 21:26:32: #1 tags after filtering in treatment: 5280878 INFO @ Sun, 21 Jun 2020 21:26:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:26:32: #1 finished! INFO @ Sun, 21 Jun 2020 21:26:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:26:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:26:32: #2 number of paired peaks: 345 WARNING @ Sun, 21 Jun 2020 21:26:32: Fewer paired peaks (345) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 345 pairs to build model! INFO @ Sun, 21 Jun 2020 21:26:32: start model_add_line... INFO @ Sun, 21 Jun 2020 21:26:32: start X-correlation... INFO @ Sun, 21 Jun 2020 21:26:32: end of X-cor INFO @ Sun, 21 Jun 2020 21:26:32: #2 finished! INFO @ Sun, 21 Jun 2020 21:26:32: #2 predicted fragment length is 11 bps INFO @ Sun, 21 Jun 2020 21:26:32: #2 alternative fragment length(s) may be 11,43,70,522,539,591 bps INFO @ Sun, 21 Jun 2020 21:26:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495188/SRX495188.20_model.r WARNING @ Sun, 21 Jun 2020 21:26:32: #2 Since the d (11) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:26:32: #2 You may need to consider one of the other alternative d(s): 11,43,70,522,539,591 WARNING @ Sun, 21 Jun 2020 21:26:32: #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 21:26:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:26:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:26:45: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:26:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495188/SRX495188.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:26:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495188/SRX495188.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:26:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495188/SRX495188.20_summits.bed INFO @ Sun, 21 Jun 2020 21:26:51: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling