Job ID = 5791247 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,381,767 reads read : 10,763,534 reads written : 10,763,534 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: 00:01:59 5381767 reads; of these: 5381767 (100.00%) were paired; of these: 370146 (6.88%) aligned concordantly 0 times 4239501 (78.78%) aligned concordantly exactly 1 time 772120 (14.35%) aligned concordantly >1 times ---- 370146 pairs aligned concordantly 0 times; of these: 83946 (22.68%) aligned discordantly 1 time ---- 286200 pairs aligned 0 times concordantly or discordantly; of these: 572400 mates make up the pairs; of these: 436452 (76.25%) aligned 0 times 85809 (14.99%) aligned exactly 1 time 50139 (8.76%) aligned >1 times 95.95% overall alignment rate Time searching: 00:01:59 Overall time: 00:01:59 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] 1712269 / 5029969 = 0.3404 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 09:17:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388390/SRX7388390.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388390/SRX7388390.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388390/SRX7388390.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388390/SRX7388390.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 09:17:07: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:17:07: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:17:12: 1000000 INFO @ Wed, 22 Apr 2020 09:17:16: 2000000 INFO @ Wed, 22 Apr 2020 09:17:21: 3000000 INFO @ Wed, 22 Apr 2020 09:17:25: 4000000 INFO @ Wed, 22 Apr 2020 09:17:29: 5000000 INFO @ Wed, 22 Apr 2020 09:17:34: 6000000 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 09:17:37: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:17:37: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:17:37: #1 total tags in treatment: 3301370 INFO @ Wed, 22 Apr 2020 09:17:37: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:17:37: #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 09:17:37: #1 tags after filtering in treatment: 1861761 INFO @ Wed, 22 Apr 2020 09:17:37: #1 Redundant rate of treatment: 0.44 INFO @ Wed, 22 Apr 2020 09:17:37: #1 finished! INFO @ Wed, 22 Apr 2020 09:17:37: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:17:37: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:17:38: #2 number of paired peaks: 138 WARNING @ Wed, 22 Apr 2020 09:17:38: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Wed, 22 Apr 2020 09:17:38: start model_add_line... INFO @ Wed, 22 Apr 2020 09:17:38: start X-correlation... INFO @ Wed, 22 Apr 2020 09:17:38: end of X-cor INFO @ Wed, 22 Apr 2020 09:17:38: #2 finished! INFO @ Wed, 22 Apr 2020 09:17:38: #2 predicted fragment length is 73 bps INFO @ Wed, 22 Apr 2020 09:17:38: #2 alternative fragment length(s) may be 73,499,513,540 bps INFO @ Wed, 22 Apr 2020 09:17:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388390/SRX7388390.05_model.r INFO @ Wed, 22 Apr 2020 09:17:38: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:17:38: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:17:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388390/SRX7388390.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388390/SRX7388390.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388390/SRX7388390.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388390/SRX7388390.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 09:17:38: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:17:38: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:17:41: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:17:43: 1000000 INFO @ Wed, 22 Apr 2020 09:17:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388390/SRX7388390.05_peaks.xls INFO @ Wed, 22 Apr 2020 09:17:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388390/SRX7388390.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:17:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388390/SRX7388390.05_summits.bed INFO @ Wed, 22 Apr 2020 09:17:43: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (3187 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:17:47: 2000000 INFO @ Wed, 22 Apr 2020 09:17:51: 3000000 INFO @ Wed, 22 Apr 2020 09:17:55: 4000000 INFO @ Wed, 22 Apr 2020 09:17:59: 5000000 INFO @ Wed, 22 Apr 2020 09:18:04: 6000000 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 09:18:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388390/SRX7388390.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388390/SRX7388390.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388390/SRX7388390.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388390/SRX7388390.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 09:18:06: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:18:06: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:18:07: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:18:07: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:18:07: #1 total tags in treatment: 3301370 INFO @ Wed, 22 Apr 2020 09:18:07: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:18:07: #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 09:18:08: #1 tags after filtering in treatment: 1861761 INFO @ Wed, 22 Apr 2020 09:18:08: #1 Redundant rate of treatment: 0.44 INFO @ Wed, 22 Apr 2020 09:18:08: #1 finished! INFO @ Wed, 22 Apr 2020 09:18:08: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:18:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:18:08: #2 number of paired peaks: 138 WARNING @ Wed, 22 Apr 2020 09:18:08: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Wed, 22 Apr 2020 09:18:08: start model_add_line... INFO @ Wed, 22 Apr 2020 09:18:08: start X-correlation... INFO @ Wed, 22 Apr 2020 09:18:08: end of X-cor INFO @ Wed, 22 Apr 2020 09:18:08: #2 finished! INFO @ Wed, 22 Apr 2020 09:18:08: #2 predicted fragment length is 73 bps INFO @ Wed, 22 Apr 2020 09:18:08: #2 alternative fragment length(s) may be 73,499,513,540 bps INFO @ Wed, 22 Apr 2020 09:18:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388390/SRX7388390.10_model.r INFO @ Wed, 22 Apr 2020 09:18:08: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:18:08: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:18:10: 1000000 INFO @ Wed, 22 Apr 2020 09:18:12: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:18:13: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388390/SRX7388390.10_peaks.xls INFO @ Wed, 22 Apr 2020 09:18:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388390/SRX7388390.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:18:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388390/SRX7388390.10_summits.bed INFO @ Wed, 22 Apr 2020 09:18:13: Done! INFO @ Wed, 22 Apr 2020 09:18:15: 2000000 pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1911 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:18:19: 3000000 INFO @ Wed, 22 Apr 2020 09:18:23: 4000000 INFO @ Wed, 22 Apr 2020 09:18:27: 5000000 INFO @ Wed, 22 Apr 2020 09:18:31: 6000000 INFO @ Wed, 22 Apr 2020 09:18:35: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:18:35: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:18:35: #1 total tags in treatment: 3301370 INFO @ Wed, 22 Apr 2020 09:18:35: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:18:35: #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 09:18:35: #1 tags after filtering in treatment: 1861761 INFO @ Wed, 22 Apr 2020 09:18:35: #1 Redundant rate of treatment: 0.44 INFO @ Wed, 22 Apr 2020 09:18:35: #1 finished! INFO @ Wed, 22 Apr 2020 09:18:35: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:18:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:18:35: #2 number of paired peaks: 138 WARNING @ Wed, 22 Apr 2020 09:18:35: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Wed, 22 Apr 2020 09:18:35: start model_add_line... INFO @ Wed, 22 Apr 2020 09:18:35: start X-correlation... INFO @ Wed, 22 Apr 2020 09:18:35: end of X-cor INFO @ Wed, 22 Apr 2020 09:18:35: #2 finished! INFO @ Wed, 22 Apr 2020 09:18:35: #2 predicted fragment length is 73 bps INFO @ Wed, 22 Apr 2020 09:18:35: #2 alternative fragment length(s) may be 73,499,513,540 bps INFO @ Wed, 22 Apr 2020 09:18:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388390/SRX7388390.20_model.r INFO @ Wed, 22 Apr 2020 09:18:35: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:18:35: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:18:39: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:18:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388390/SRX7388390.20_peaks.xls INFO @ Wed, 22 Apr 2020 09:18:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388390/SRX7388390.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:18:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388390/SRX7388390.20_summits.bed INFO @ Wed, 22 Apr 2020 09:18:41: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (517 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。