Job ID = 5790856 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,054,869 reads read : 4,109,738 reads written : 4,109,738 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: 00:00:55 2054869 reads; of these: 2054869 (100.00%) were paired; of these: 59722 (2.91%) aligned concordantly 0 times 1694476 (82.46%) aligned concordantly exactly 1 time 300671 (14.63%) aligned concordantly >1 times ---- 59722 pairs aligned concordantly 0 times; of these: 1531 (2.56%) aligned discordantly 1 time ---- 58191 pairs aligned 0 times concordantly or discordantly; of these: 116382 mates make up the pairs; of these: 101402 (87.13%) aligned 0 times 11512 (9.89%) aligned exactly 1 time 3468 (2.98%) aligned >1 times 97.53% overall alignment rate Time searching: 00:00:55 Overall time: 00:00:55 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] 56581 / 1995835 = 0.0283 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 07:57:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5521504/SRX5521504.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5521504/SRX5521504.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5521504/SRX5521504.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5521504/SRX5521504.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 07:57:34: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:57:34: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:57:39: 1000000 INFO @ Wed, 22 Apr 2020 07:57:44: 2000000 INFO @ Wed, 22 Apr 2020 07:57:49: 3000000 INFO @ Wed, 22 Apr 2020 07:57:53: #1 tag size is determined as 36 bps INFO @ Wed, 22 Apr 2020 07:57:53: #1 tag size = 36 INFO @ Wed, 22 Apr 2020 07:57:53: #1 total tags in treatment: 1938575 INFO @ Wed, 22 Apr 2020 07:57:53: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:57:53: #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 07:57:53: #1 tags after filtering in treatment: 1626579 INFO @ Wed, 22 Apr 2020 07:57:53: #1 Redundant rate of treatment: 0.16 INFO @ Wed, 22 Apr 2020 07:57:53: #1 finished! INFO @ Wed, 22 Apr 2020 07:57:53: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:57:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:57:53: #2 number of paired peaks: 104 WARNING @ Wed, 22 Apr 2020 07:57:53: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Wed, 22 Apr 2020 07:57:53: start model_add_line... INFO @ Wed, 22 Apr 2020 07:57:53: start X-correlation... INFO @ Wed, 22 Apr 2020 07:57:53: end of X-cor INFO @ Wed, 22 Apr 2020 07:57:53: #2 finished! INFO @ Wed, 22 Apr 2020 07:57:53: #2 predicted fragment length is 159 bps INFO @ Wed, 22 Apr 2020 07:57:53: #2 alternative fragment length(s) may be 159 bps INFO @ Wed, 22 Apr 2020 07:57:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5521504/SRX5521504.05_model.r INFO @ Wed, 22 Apr 2020 07:57:53: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:57:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:57:57: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:57:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5521504/SRX5521504.05_peaks.xls INFO @ Wed, 22 Apr 2020 07:57:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5521504/SRX5521504.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:57:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5521504/SRX5521504.05_summits.bed INFO @ Wed, 22 Apr 2020 07:57:58: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (394 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 07:58:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5521504/SRX5521504.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5521504/SRX5521504.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5521504/SRX5521504.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5521504/SRX5521504.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 07:58:04: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:58:04: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:58:09: 1000000 INFO @ Wed, 22 Apr 2020 07:58:14: 2000000 INFO @ Wed, 22 Apr 2020 07:58:19: 3000000 INFO @ Wed, 22 Apr 2020 07:58:23: #1 tag size is determined as 36 bps INFO @ Wed, 22 Apr 2020 07:58:23: #1 tag size = 36 INFO @ Wed, 22 Apr 2020 07:58:23: #1 total tags in treatment: 1938575 INFO @ Wed, 22 Apr 2020 07:58:23: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:58:23: #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 07:58:23: #1 tags after filtering in treatment: 1626579 INFO @ Wed, 22 Apr 2020 07:58:23: #1 Redundant rate of treatment: 0.16 INFO @ Wed, 22 Apr 2020 07:58:23: #1 finished! INFO @ Wed, 22 Apr 2020 07:58:23: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:58:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:58:23: #2 number of paired peaks: 104 WARNING @ Wed, 22 Apr 2020 07:58:23: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Wed, 22 Apr 2020 07:58:23: start model_add_line... INFO @ Wed, 22 Apr 2020 07:58:23: start X-correlation... INFO @ Wed, 22 Apr 2020 07:58:23: end of X-cor INFO @ Wed, 22 Apr 2020 07:58:23: #2 finished! INFO @ Wed, 22 Apr 2020 07:58:23: #2 predicted fragment length is 159 bps INFO @ Wed, 22 Apr 2020 07:58:23: #2 alternative fragment length(s) may be 159 bps INFO @ Wed, 22 Apr 2020 07:58:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5521504/SRX5521504.10_model.r INFO @ Wed, 22 Apr 2020 07:58:23: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:58:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:58:27: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:58:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5521504/SRX5521504.10_peaks.xls INFO @ Wed, 22 Apr 2020 07:58:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5521504/SRX5521504.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:58:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5521504/SRX5521504.10_summits.bed INFO @ Wed, 22 Apr 2020 07:58:28: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (284 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 07:58:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5521504/SRX5521504.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5521504/SRX5521504.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5521504/SRX5521504.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5521504/SRX5521504.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 07:58:34: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:58:34: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:58:39: 1000000 INFO @ Wed, 22 Apr 2020 07:58:44: 2000000 INFO @ Wed, 22 Apr 2020 07:58:49: 3000000 INFO @ Wed, 22 Apr 2020 07:58:53: #1 tag size is determined as 36 bps INFO @ Wed, 22 Apr 2020 07:58:53: #1 tag size = 36 INFO @ Wed, 22 Apr 2020 07:58:53: #1 total tags in treatment: 1938575 INFO @ Wed, 22 Apr 2020 07:58:53: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:58:53: #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 07:58:53: #1 tags after filtering in treatment: 1626579 INFO @ Wed, 22 Apr 2020 07:58:53: #1 Redundant rate of treatment: 0.16 INFO @ Wed, 22 Apr 2020 07:58:53: #1 finished! INFO @ Wed, 22 Apr 2020 07:58:53: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:58:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:58:53: #2 number of paired peaks: 104 WARNING @ Wed, 22 Apr 2020 07:58:53: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Wed, 22 Apr 2020 07:58:53: start model_add_line... INFO @ Wed, 22 Apr 2020 07:58:53: start X-correlation... INFO @ Wed, 22 Apr 2020 07:58:53: end of X-cor INFO @ Wed, 22 Apr 2020 07:58:53: #2 finished! INFO @ Wed, 22 Apr 2020 07:58:53: #2 predicted fragment length is 159 bps INFO @ Wed, 22 Apr 2020 07:58:53: #2 alternative fragment length(s) may be 159 bps INFO @ Wed, 22 Apr 2020 07:58:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5521504/SRX5521504.20_model.r INFO @ Wed, 22 Apr 2020 07:58:53: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:58:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:58:57: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:58:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5521504/SRX5521504.20_peaks.xls INFO @ Wed, 22 Apr 2020 07:58:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5521504/SRX5521504.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:58:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5521504/SRX5521504.20_summits.bed INFO @ Wed, 22 Apr 2020 07:58:58: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (172 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。