Job ID = 7113464 SRX = SRX8462170 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T05:37:55 prefetch.2.10.7: 1) Downloading 'SRR11915629'... 2020-07-22T05:37:55 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T05:39:46 prefetch.2.10.7: HTTPS download succeed 2020-07-22T05:39:47 prefetch.2.10.7: 'SRR11915629' is valid 2020-07-22T05:39:47 prefetch.2.10.7: 1) 'SRR11915629' was downloaded successfully 2020-07-22T05:39:47 prefetch.2.10.7: 'SRR11915629' has 0 unresolved dependencies Read 6815201 spots for SRR11915629/SRR11915629.sra Written 6815201 spots for SRR11915629/SRR11915629.sra 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: 00:02:40 6815201 reads; of these: 6815201 (100.00%) were paired; of these: 4241232 (62.23%) aligned concordantly 0 times 2167368 (31.80%) aligned concordantly exactly 1 time 406601 (5.97%) aligned concordantly >1 times ---- 4241232 pairs aligned concordantly 0 times; of these: 13864 (0.33%) aligned discordantly 1 time ---- 4227368 pairs aligned 0 times concordantly or discordantly; of these: 8454736 mates make up the pairs; of these: 8397722 (99.33%) aligned 0 times 42373 (0.50%) aligned exactly 1 time 14641 (0.17%) aligned >1 times 38.39% overall alignment rate Time searching: 00:02:40 Overall time: 00:02:40 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] 2308891 / 2587686 = 0.8923 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 Jul 2020 14:44:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462170/SRX8462170.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462170/SRX8462170.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462170/SRX8462170.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462170/SRX8462170.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 Jul 2020 14:44:34: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:44:34: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:44:38: #1 tag size is determined as 76 bps INFO @ Wed, 22 Jul 2020 14:44:38: #1 tag size = 76 INFO @ Wed, 22 Jul 2020 14:44:38: #1 total tags in treatment: 274715 INFO @ Wed, 22 Jul 2020 14:44:38: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:44:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 14:44:38: #1 tags after filtering in treatment: 214448 INFO @ Wed, 22 Jul 2020 14:44:38: #1 Redundant rate of treatment: 0.22 INFO @ Wed, 22 Jul 2020 14:44:38: #1 finished! INFO @ Wed, 22 Jul 2020 14:44:38: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:44:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:44:38: #2 number of paired peaks: 209 WARNING @ Wed, 22 Jul 2020 14:44:38: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Wed, 22 Jul 2020 14:44:38: start model_add_line... INFO @ Wed, 22 Jul 2020 14:44:38: start X-correlation... INFO @ Wed, 22 Jul 2020 14:44:38: end of X-cor INFO @ Wed, 22 Jul 2020 14:44:38: #2 finished! INFO @ Wed, 22 Jul 2020 14:44:38: #2 predicted fragment length is 247 bps INFO @ Wed, 22 Jul 2020 14:44:38: #2 alternative fragment length(s) may be 99,124,152,185,211,247,302,319,391,438,489,537,578,584 bps INFO @ Wed, 22 Jul 2020 14:44:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8462170/SRX8462170.05_model.r INFO @ Wed, 22 Jul 2020 14:44:38: #3 Call peaks... INFO @ Wed, 22 Jul 2020 14:44:38: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 14:44:38: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 14:44:39: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8462170/SRX8462170.05_peaks.xls INFO @ Wed, 22 Jul 2020 14:44:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8462170/SRX8462170.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 14:44:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8462170/SRX8462170.05_summits.bed INFO @ Wed, 22 Jul 2020 14:44:39: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (33 records, 4 fields): 1 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 Jul 2020 14:45:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462170/SRX8462170.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462170/SRX8462170.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462170/SRX8462170.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462170/SRX8462170.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 Jul 2020 14:45:04: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:45:04: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 14:45:09: #1 tag size is determined as 76 bps INFO @ Wed, 22 Jul 2020 14:45:09: #1 tag size = 76 INFO @ Wed, 22 Jul 2020 14:45:09: #1 total tags in treatment: 274715 INFO @ Wed, 22 Jul 2020 14:45:09: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:45:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 14:45:09: #1 tags after filtering in treatment: 214448 INFO @ Wed, 22 Jul 2020 14:45:09: #1 Redundant rate of treatment: 0.22 INFO @ Wed, 22 Jul 2020 14:45:09: #1 finished! INFO @ Wed, 22 Jul 2020 14:45:09: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:45:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:45:09: #2 number of paired peaks: 209 WARNING @ Wed, 22 Jul 2020 14:45:09: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Wed, 22 Jul 2020 14:45:09: start model_add_line... INFO @ Wed, 22 Jul 2020 14:45:09: start X-correlation... INFO @ Wed, 22 Jul 2020 14:45:09: end of X-cor INFO @ Wed, 22 Jul 2020 14:45:09: #2 finished! INFO @ Wed, 22 Jul 2020 14:45:09: #2 predicted fragment length is 247 bps INFO @ Wed, 22 Jul 2020 14:45:09: #2 alternative fragment length(s) may be 99,124,152,185,211,247,302,319,391,438,489,537,578,584 bps INFO @ Wed, 22 Jul 2020 14:45:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8462170/SRX8462170.10_model.r INFO @ Wed, 22 Jul 2020 14:45:09: #3 Call peaks... INFO @ Wed, 22 Jul 2020 14:45:09: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 14:45:10: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 14:45:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8462170/SRX8462170.10_peaks.xls INFO @ Wed, 22 Jul 2020 14:45:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8462170/SRX8462170.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 14:45:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8462170/SRX8462170.10_summits.bed INFO @ Wed, 22 Jul 2020 14:45:10: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (6 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 Jul 2020 14:45:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8462170/SRX8462170.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8462170/SRX8462170.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8462170/SRX8462170.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8462170/SRX8462170.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 Jul 2020 14:45:34: #1 read tag files... INFO @ Wed, 22 Jul 2020 14:45:34: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 14:45:39: #1 tag size is determined as 76 bps INFO @ Wed, 22 Jul 2020 14:45:39: #1 tag size = 76 INFO @ Wed, 22 Jul 2020 14:45:39: #1 total tags in treatment: 274715 INFO @ Wed, 22 Jul 2020 14:45:39: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 14:45:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 14:45:39: #1 tags after filtering in treatment: 214448 INFO @ Wed, 22 Jul 2020 14:45:39: #1 Redundant rate of treatment: 0.22 INFO @ Wed, 22 Jul 2020 14:45:39: #1 finished! INFO @ Wed, 22 Jul 2020 14:45:39: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 14:45:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 14:45:39: #2 number of paired peaks: 209 WARNING @ Wed, 22 Jul 2020 14:45:39: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Wed, 22 Jul 2020 14:45:39: start model_add_line... INFO @ Wed, 22 Jul 2020 14:45:39: start X-correlation... INFO @ Wed, 22 Jul 2020 14:45:39: end of X-cor INFO @ Wed, 22 Jul 2020 14:45:39: #2 finished! INFO @ Wed, 22 Jul 2020 14:45:39: #2 predicted fragment length is 247 bps INFO @ Wed, 22 Jul 2020 14:45:39: #2 alternative fragment length(s) may be 99,124,152,185,211,247,302,319,391,438,489,537,578,584 bps INFO @ Wed, 22 Jul 2020 14:45:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8462170/SRX8462170.20_model.r INFO @ Wed, 22 Jul 2020 14:45:39: #3 Call peaks... INFO @ Wed, 22 Jul 2020 14:45:39: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 14:45:40: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 14:45:40: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8462170/SRX8462170.20_peaks.xls INFO @ Wed, 22 Jul 2020 14:45:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8462170/SRX8462170.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 14:45:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8462170/SRX8462170.20_summits.bed INFO @ Wed, 22 Jul 2020 14:45:40: Done! pass1 - making usageList (1 chroms): 0 millis pass2 - checking and writing primary data (1 records, 4 fields): 1 millis CompletedMACS2peakCalling