Job ID = 5791764 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,112,808 reads read : 6,225,616 reads written : 6,225,616 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: 00:02:09 3112808 reads; of these: 3112808 (100.00%) were paired; of these: 303708 (9.76%) aligned concordantly 0 times 2527299 (81.19%) aligned concordantly exactly 1 time 281801 (9.05%) aligned concordantly >1 times ---- 303708 pairs aligned concordantly 0 times; of these: 187113 (61.61%) aligned discordantly 1 time ---- 116595 pairs aligned 0 times concordantly or discordantly; of these: 233190 mates make up the pairs; of these: 153639 (65.89%) aligned 0 times 32064 (13.75%) aligned exactly 1 time 47487 (20.36%) aligned >1 times 97.53% overall alignment rate Time searching: 00:02:09 Overall time: 00:02:09 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] 77069 / 2992286 = 0.0258 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 10:46:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7741029/SRX7741029.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7741029/SRX7741029.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7741029/SRX7741029.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7741029/SRX7741029.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 10:46:32: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:46:32: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:46:38: 1000000 INFO @ Wed, 22 Apr 2020 10:46:43: 2000000 INFO @ Wed, 22 Apr 2020 10:46:49: 3000000 INFO @ Wed, 22 Apr 2020 10:46:55: 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 @ Wed, 22 Apr 2020 10:47:00: 5000000 INFO @ Wed, 22 Apr 2020 10:47:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7741029/SRX7741029.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7741029/SRX7741029.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7741029/SRX7741029.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7741029/SRX7741029.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 10:47:01: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:47:01: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:47:06: #1 tag size is determined as 80 bps INFO @ Wed, 22 Apr 2020 10:47:06: #1 tag size = 80 INFO @ Wed, 22 Apr 2020 10:47:06: #1 total tags in treatment: 2734961 INFO @ Wed, 22 Apr 2020 10:47:06: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:47:06: #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 10:47:06: #1 tags after filtering in treatment: 2345038 INFO @ Wed, 22 Apr 2020 10:47:06: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 22 Apr 2020 10:47:06: #1 finished! INFO @ Wed, 22 Apr 2020 10:47:06: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:47:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:47:06: #2 number of paired peaks: 197 WARNING @ Wed, 22 Apr 2020 10:47:06: Fewer paired peaks (197) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 197 pairs to build model! INFO @ Wed, 22 Apr 2020 10:47:06: start model_add_line... INFO @ Wed, 22 Apr 2020 10:47:06: start X-correlation... INFO @ Wed, 22 Apr 2020 10:47:06: end of X-cor INFO @ Wed, 22 Apr 2020 10:47:06: #2 finished! INFO @ Wed, 22 Apr 2020 10:47:06: #2 predicted fragment length is 327 bps INFO @ Wed, 22 Apr 2020 10:47:06: #2 alternative fragment length(s) may be 1,280,303,327,339,370 bps INFO @ Wed, 22 Apr 2020 10:47:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7741029/SRX7741029.05_model.r INFO @ Wed, 22 Apr 2020 10:47:06: #3 Call peaks... INFO @ Wed, 22 Apr 2020 10:47:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 10:47:08: 1000000 INFO @ Wed, 22 Apr 2020 10:47:12: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 10:47:14: 2000000 INFO @ Wed, 22 Apr 2020 10:47:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7741029/SRX7741029.05_peaks.xls INFO @ Wed, 22 Apr 2020 10:47:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7741029/SRX7741029.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 10:47:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7741029/SRX7741029.05_summits.bed INFO @ Wed, 22 Apr 2020 10:47:14: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1013 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:47:20: 3000000 INFO @ Wed, 22 Apr 2020 10:47:27: 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 10:47:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7741029/SRX7741029.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7741029/SRX7741029.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7741029/SRX7741029.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7741029/SRX7741029.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 10:47:31: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:47:31: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:47:33: 5000000 INFO @ Wed, 22 Apr 2020 10:47:38: 1000000 INFO @ Wed, 22 Apr 2020 10:47:38: #1 tag size is determined as 80 bps INFO @ Wed, 22 Apr 2020 10:47:38: #1 tag size = 80 INFO @ Wed, 22 Apr 2020 10:47:38: #1 total tags in treatment: 2734961 INFO @ Wed, 22 Apr 2020 10:47:38: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:47:38: #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 10:47:38: #1 tags after filtering in treatment: 2345038 INFO @ Wed, 22 Apr 2020 10:47:38: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 22 Apr 2020 10:47:38: #1 finished! INFO @ Wed, 22 Apr 2020 10:47:38: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:47:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:47:39: #2 number of paired peaks: 197 WARNING @ Wed, 22 Apr 2020 10:47:39: Fewer paired peaks (197) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 197 pairs to build model! INFO @ Wed, 22 Apr 2020 10:47:39: start model_add_line... INFO @ Wed, 22 Apr 2020 10:47:39: start X-correlation... INFO @ Wed, 22 Apr 2020 10:47:39: end of X-cor INFO @ Wed, 22 Apr 2020 10:47:39: #2 finished! INFO @ Wed, 22 Apr 2020 10:47:39: #2 predicted fragment length is 327 bps INFO @ Wed, 22 Apr 2020 10:47:39: #2 alternative fragment length(s) may be 1,280,303,327,339,370 bps INFO @ Wed, 22 Apr 2020 10:47:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7741029/SRX7741029.10_model.r INFO @ Wed, 22 Apr 2020 10:47:39: #3 Call peaks... INFO @ Wed, 22 Apr 2020 10:47:39: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 10:47:44: 2000000 INFO @ Wed, 22 Apr 2020 10:47:45: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 10:47:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7741029/SRX7741029.10_peaks.xls INFO @ Wed, 22 Apr 2020 10:47:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7741029/SRX7741029.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 10:47:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7741029/SRX7741029.10_summits.bed INFO @ Wed, 22 Apr 2020 10:47:47: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (600 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:47:49: 3000000 INFO @ Wed, 22 Apr 2020 10:47:55: 4000000 INFO @ Wed, 22 Apr 2020 10:48:01: 5000000 INFO @ Wed, 22 Apr 2020 10:48:06: #1 tag size is determined as 80 bps INFO @ Wed, 22 Apr 2020 10:48:06: #1 tag size = 80 INFO @ Wed, 22 Apr 2020 10:48:06: #1 total tags in treatment: 2734961 INFO @ Wed, 22 Apr 2020 10:48:06: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:48:06: #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 10:48:06: #1 tags after filtering in treatment: 2345038 INFO @ Wed, 22 Apr 2020 10:48:06: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 22 Apr 2020 10:48:06: #1 finished! INFO @ Wed, 22 Apr 2020 10:48:06: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:48:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:48:06: #2 number of paired peaks: 197 WARNING @ Wed, 22 Apr 2020 10:48:06: Fewer paired peaks (197) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 197 pairs to build model! INFO @ Wed, 22 Apr 2020 10:48:06: start model_add_line... INFO @ Wed, 22 Apr 2020 10:48:06: start X-correlation... INFO @ Wed, 22 Apr 2020 10:48:06: end of X-cor INFO @ Wed, 22 Apr 2020 10:48:06: #2 finished! INFO @ Wed, 22 Apr 2020 10:48:06: #2 predicted fragment length is 327 bps INFO @ Wed, 22 Apr 2020 10:48:06: #2 alternative fragment length(s) may be 1,280,303,327,339,370 bps INFO @ Wed, 22 Apr 2020 10:48:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7741029/SRX7741029.20_model.r INFO @ Wed, 22 Apr 2020 10:48:06: #3 Call peaks... INFO @ Wed, 22 Apr 2020 10:48:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 10:48:12: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 10:48:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7741029/SRX7741029.20_peaks.xls INFO @ Wed, 22 Apr 2020 10:48:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7741029/SRX7741029.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 10:48:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7741029/SRX7741029.20_summits.bed INFO @ Wed, 22 Apr 2020 10:48:14: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (362 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。