Job ID = 5790989 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,520,717 reads read : 5,041,434 reads written : 5,041,434 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: 00:02:05 2520717 reads; of these: 2520717 (100.00%) were paired; of these: 153511 (6.09%) aligned concordantly 0 times 1721447 (68.29%) aligned concordantly exactly 1 time 645759 (25.62%) aligned concordantly >1 times ---- 153511 pairs aligned concordantly 0 times; of these: 1317 (0.86%) aligned discordantly 1 time ---- 152194 pairs aligned 0 times concordantly or discordantly; of these: 304388 mates make up the pairs; of these: 283534 (93.15%) aligned 0 times 12039 (3.96%) aligned exactly 1 time 8815 (2.90%) aligned >1 times 94.38% overall alignment rate Time searching: 00:02:05 Overall time: 00:02:05 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] 48442 / 2365649 = 0.0205 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 08:15:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874488/SRX5874488.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874488/SRX5874488.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874488/SRX5874488.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874488/SRX5874488.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 08:15:01: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:15:01: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:15:06: 1000000 INFO @ Wed, 22 Apr 2020 08:15:12: 2000000 INFO @ Wed, 22 Apr 2020 08:15:18: 3000000 INFO @ Wed, 22 Apr 2020 08:15:24: 4000000 INFO @ Wed, 22 Apr 2020 08:15:28: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:15:28: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:15:28: #1 total tags in treatment: 2318766 INFO @ Wed, 22 Apr 2020 08:15:28: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:15:28: #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 08:15:28: #1 tags after filtering in treatment: 1905112 INFO @ Wed, 22 Apr 2020 08:15:28: #1 Redundant rate of treatment: 0.18 INFO @ Wed, 22 Apr 2020 08:15:28: #1 finished! INFO @ Wed, 22 Apr 2020 08:15:28: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:15:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:15:28: #2 number of paired peaks: 324 WARNING @ Wed, 22 Apr 2020 08:15:28: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Wed, 22 Apr 2020 08:15:28: start model_add_line... INFO @ Wed, 22 Apr 2020 08:15:28: start X-correlation... INFO @ Wed, 22 Apr 2020 08:15:28: end of X-cor INFO @ Wed, 22 Apr 2020 08:15:28: #2 finished! INFO @ Wed, 22 Apr 2020 08:15:28: #2 predicted fragment length is 157 bps INFO @ Wed, 22 Apr 2020 08:15:28: #2 alternative fragment length(s) may be 3,136,157 bps INFO @ Wed, 22 Apr 2020 08:15:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874488/SRX5874488.05_model.r INFO @ Wed, 22 Apr 2020 08:15:28: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:15:28: #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 08:15:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874488/SRX5874488.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874488/SRX5874488.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874488/SRX5874488.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874488/SRX5874488.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 08:15:31: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:15:31: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:15:33: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:15:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874488/SRX5874488.05_peaks.xls INFO @ Wed, 22 Apr 2020 08:15:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874488/SRX5874488.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:15:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874488/SRX5874488.05_summits.bed INFO @ Wed, 22 Apr 2020 08:15:35: Done! INFO @ Wed, 22 Apr 2020 08:15:37: 1000000 pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (539 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:15:43: 2000000 INFO @ Wed, 22 Apr 2020 08:15:48: 3000000 INFO @ Wed, 22 Apr 2020 08:15:54: 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 08:15:58: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:15:58: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:15:58: #1 total tags in treatment: 2318766 INFO @ Wed, 22 Apr 2020 08:15:58: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:15:58: #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 08:15:58: #1 tags after filtering in treatment: 1905112 INFO @ Wed, 22 Apr 2020 08:15:58: #1 Redundant rate of treatment: 0.18 INFO @ Wed, 22 Apr 2020 08:15:58: #1 finished! INFO @ Wed, 22 Apr 2020 08:15:58: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:15:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:15:58: #2 number of paired peaks: 324 WARNING @ Wed, 22 Apr 2020 08:15:58: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Wed, 22 Apr 2020 08:15:58: start model_add_line... INFO @ Wed, 22 Apr 2020 08:15:58: start X-correlation... INFO @ Wed, 22 Apr 2020 08:15:58: end of X-cor INFO @ Wed, 22 Apr 2020 08:15:58: #2 finished! INFO @ Wed, 22 Apr 2020 08:15:58: #2 predicted fragment length is 157 bps INFO @ Wed, 22 Apr 2020 08:15:58: #2 alternative fragment length(s) may be 3,136,157 bps INFO @ Wed, 22 Apr 2020 08:15:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874488/SRX5874488.10_model.r INFO @ Wed, 22 Apr 2020 08:15:58: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:15:58: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:16:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874488/SRX5874488.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874488/SRX5874488.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874488/SRX5874488.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874488/SRX5874488.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 08:16:01: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:16:01: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:16:04: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:16:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874488/SRX5874488.10_peaks.xls INFO @ Wed, 22 Apr 2020 08:16:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874488/SRX5874488.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:16:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874488/SRX5874488.10_summits.bed INFO @ Wed, 22 Apr 2020 08:16:05: Done! INFO @ Wed, 22 Apr 2020 08:16:07: 1000000 pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (361 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:16:13: 2000000 INFO @ Wed, 22 Apr 2020 08:16:19: 3000000 INFO @ Wed, 22 Apr 2020 08:16:25: 4000000 INFO @ Wed, 22 Apr 2020 08:16:29: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:16:29: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:16:29: #1 total tags in treatment: 2318766 INFO @ Wed, 22 Apr 2020 08:16:29: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:16:29: #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 08:16:29: #1 tags after filtering in treatment: 1905112 INFO @ Wed, 22 Apr 2020 08:16:29: #1 Redundant rate of treatment: 0.18 INFO @ Wed, 22 Apr 2020 08:16:29: #1 finished! INFO @ Wed, 22 Apr 2020 08:16:29: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:16:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:16:29: #2 number of paired peaks: 324 WARNING @ Wed, 22 Apr 2020 08:16:29: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Wed, 22 Apr 2020 08:16:29: start model_add_line... INFO @ Wed, 22 Apr 2020 08:16:29: start X-correlation... INFO @ Wed, 22 Apr 2020 08:16:29: end of X-cor INFO @ Wed, 22 Apr 2020 08:16:29: #2 finished! INFO @ Wed, 22 Apr 2020 08:16:29: #2 predicted fragment length is 157 bps INFO @ Wed, 22 Apr 2020 08:16:29: #2 alternative fragment length(s) may be 3,136,157 bps INFO @ Wed, 22 Apr 2020 08:16:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874488/SRX5874488.20_model.r INFO @ Wed, 22 Apr 2020 08:16:29: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:16:29: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:16:35: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 08:16:37: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874488/SRX5874488.20_peaks.xls INFO @ Wed, 22 Apr 2020 08:16:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874488/SRX5874488.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:16:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874488/SRX5874488.20_summits.bed INFO @ Wed, 22 Apr 2020 08:16:37: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (185 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。