Job ID = 5790859 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,924,345 reads read : 5,848,690 reads written : 5,848,690 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:01:30 2924345 reads; of these: 2924345 (100.00%) were paired; of these: 62672 (2.14%) aligned concordantly 0 times 2465425 (84.31%) aligned concordantly exactly 1 time 396248 (13.55%) aligned concordantly >1 times ---- 62672 pairs aligned concordantly 0 times; of these: 7553 (12.05%) aligned discordantly 1 time ---- 55119 pairs aligned 0 times concordantly or discordantly; of these: 110238 mates make up the pairs; of these: 84466 (76.62%) aligned 0 times 19156 (17.38%) aligned exactly 1 time 6616 (6.00%) aligned >1 times 98.56% overall alignment rate Time searching: 00:01:30 Overall time: 00:01:30 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 127881 / 2862694 = 0.0447 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 @ Wed, 22 Apr 2020 08:00:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5521507/SRX5521507.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5521507/SRX5521507.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5521507/SRX5521507.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5521507/SRX5521507.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Wed, 22 Apr 2020 08:00:50: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:00:50: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:00:55: 1000000 INFO @ Wed, 22 Apr 2020 08:01:00: 2000000 INFO @ Wed, 22 Apr 2020 08:01:05: 3000000 INFO @ Wed, 22 Apr 2020 08:01:10: 4000000 INFO @ Wed, 22 Apr 2020 08:01:15: 5000000 INFO @ Wed, 22 Apr 2020 08:01:17: #1 tag size is determined as 36 bps INFO @ Wed, 22 Apr 2020 08:01:17: #1 tag size = 36 INFO @ Wed, 22 Apr 2020 08:01:17: #1 total tags in treatment: 2733841 INFO @ Wed, 22 Apr 2020 08:01:17: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:01:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 08:01:17: #1 tags after filtering in treatment: 2339945 INFO @ Wed, 22 Apr 2020 08:01:17: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 22 Apr 2020 08:01:17: #1 finished! INFO @ Wed, 22 Apr 2020 08:01:17: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:01:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:01:18: #2 number of paired peaks: 127 WARNING @ Wed, 22 Apr 2020 08:01:18: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Wed, 22 Apr 2020 08:01:18: start model_add_line... INFO @ Wed, 22 Apr 2020 08:01:18: start X-correlation... INFO @ Wed, 22 Apr 2020 08:01:18: end of X-cor INFO @ Wed, 22 Apr 2020 08:01:18: #2 finished! INFO @ Wed, 22 Apr 2020 08:01:18: #2 predicted fragment length is 2 bps INFO @ Wed, 22 Apr 2020 08:01:18: #2 alternative fragment length(s) may be 2,19,25 bps INFO @ Wed, 22 Apr 2020 08:01:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5521507/SRX5521507.05_model.r WARNING @ Wed, 22 Apr 2020 08:01:18: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:01:18: #2 You may need to consider one of the other alternative d(s): 2,19,25 WARNING @ Wed, 22 Apr 2020 08:01:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 08:01:18: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:01:18: #3 Pre-compute pvalue-qvalue table... 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 @ Wed, 22 Apr 2020 08:01:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5521507/SRX5521507.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5521507/SRX5521507.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5521507/SRX5521507.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5521507/SRX5521507.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Wed, 22 Apr 2020 08:01:20: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:01:20: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:01:21: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:01:22: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5521507/SRX5521507.05_peaks.xls INFO @ Wed, 22 Apr 2020 08:01:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5521507/SRX5521507.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:01:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5521507/SRX5521507.05_summits.bed INFO @ Wed, 22 Apr 2020 08:01:22: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:01:27: 1000000 INFO @ Wed, 22 Apr 2020 08:01:34: 2000000 INFO @ Wed, 22 Apr 2020 08:01:41: 3000000 INFO @ Wed, 22 Apr 2020 08:01:48: 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 @ Wed, 22 Apr 2020 08:01:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5521507/SRX5521507.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5521507/SRX5521507.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5521507/SRX5521507.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5521507/SRX5521507.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Wed, 22 Apr 2020 08:01:50: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:01:50: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:01:55: 5000000 INFO @ Wed, 22 Apr 2020 08:01:55: 1000000 INFO @ Wed, 22 Apr 2020 08:01:58: #1 tag size is determined as 36 bps INFO @ Wed, 22 Apr 2020 08:01:58: #1 tag size = 36 INFO @ Wed, 22 Apr 2020 08:01:58: #1 total tags in treatment: 2733841 INFO @ Wed, 22 Apr 2020 08:01:58: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:01:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 08:01:58: #1 tags after filtering in treatment: 2339945 INFO @ Wed, 22 Apr 2020 08:01:58: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 22 Apr 2020 08:01:58: #1 finished! INFO @ Wed, 22 Apr 2020 08:01:58: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:01:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:01:58: #2 number of paired peaks: 127 WARNING @ Wed, 22 Apr 2020 08:01:58: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Wed, 22 Apr 2020 08:01:58: start model_add_line... INFO @ Wed, 22 Apr 2020 08:01:58: start X-correlation... INFO @ Wed, 22 Apr 2020 08:01:58: end of X-cor INFO @ Wed, 22 Apr 2020 08:01:58: #2 finished! INFO @ Wed, 22 Apr 2020 08:01:58: #2 predicted fragment length is 2 bps INFO @ Wed, 22 Apr 2020 08:01:58: #2 alternative fragment length(s) may be 2,19,25 bps INFO @ Wed, 22 Apr 2020 08:01:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5521507/SRX5521507.10_model.r WARNING @ Wed, 22 Apr 2020 08:01:58: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:01:58: #2 You may need to consider one of the other alternative d(s): 2,19,25 WARNING @ Wed, 22 Apr 2020 08:01:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 08:01:58: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:01:58: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:02:00: 2000000 INFO @ Wed, 22 Apr 2020 08:02:02: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:02:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5521507/SRX5521507.10_peaks.xls INFO @ Wed, 22 Apr 2020 08:02:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5521507/SRX5521507.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:02:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5521507/SRX5521507.10_summits.bed INFO @ Wed, 22 Apr 2020 08:02:04: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:02:05: 3000000 INFO @ Wed, 22 Apr 2020 08:02:10: 4000000 INFO @ Wed, 22 Apr 2020 08:02:15: 5000000 INFO @ Wed, 22 Apr 2020 08:02:17: #1 tag size is determined as 36 bps INFO @ Wed, 22 Apr 2020 08:02:17: #1 tag size = 36 INFO @ Wed, 22 Apr 2020 08:02:17: #1 total tags in treatment: 2733841 INFO @ Wed, 22 Apr 2020 08:02:17: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:02:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 08:02:17: #1 tags after filtering in treatment: 2339945 INFO @ Wed, 22 Apr 2020 08:02:17: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 22 Apr 2020 08:02:17: #1 finished! INFO @ Wed, 22 Apr 2020 08:02:17: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:02:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:02:17: #2 number of paired peaks: 127 WARNING @ Wed, 22 Apr 2020 08:02:17: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Wed, 22 Apr 2020 08:02:17: start model_add_line... INFO @ Wed, 22 Apr 2020 08:02:17: start X-correlation... INFO @ Wed, 22 Apr 2020 08:02:17: end of X-cor INFO @ Wed, 22 Apr 2020 08:02:17: #2 finished! INFO @ Wed, 22 Apr 2020 08:02:17: #2 predicted fragment length is 2 bps INFO @ Wed, 22 Apr 2020 08:02:17: #2 alternative fragment length(s) may be 2,19,25 bps INFO @ Wed, 22 Apr 2020 08:02:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5521507/SRX5521507.20_model.r WARNING @ Wed, 22 Apr 2020 08:02:17: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:02:17: #2 You may need to consider one of the other alternative d(s): 2,19,25 WARNING @ Wed, 22 Apr 2020 08:02:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 08:02:17: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:02:17: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:02:21: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:02:22: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5521507/SRX5521507.20_peaks.xls INFO @ Wed, 22 Apr 2020 08:02:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5521507/SRX5521507.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:02:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5521507/SRX5521507.20_summits.bed INFO @ Wed, 22 Apr 2020 08:02:22: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。