Job ID = 5791273 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 15,806,276 reads read : 31,612,552 reads written : 31,612,552 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: 00:13:05 15806276 reads; of these: 15806276 (100.00%) were paired; of these: 13164544 (83.29%) aligned concordantly 0 times 828037 (5.24%) aligned concordantly exactly 1 time 1813695 (11.47%) aligned concordantly >1 times ---- 13164544 pairs aligned concordantly 0 times; of these: 1863403 (14.15%) aligned discordantly 1 time ---- 11301141 pairs aligned 0 times concordantly or discordantly; of these: 22602282 mates make up the pairs; of these: 13921138 (61.59%) aligned 0 times 2923681 (12.94%) aligned exactly 1 time 5757463 (25.47%) aligned >1 times 55.96% overall alignment rate Time searching: 00:13:05 Overall time: 00:13:05 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_sort_core] merging from 8 files... [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] 2249385 / 4369321 = 0.5148 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 09:43:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7399905/SRX7399905.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7399905/SRX7399905.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7399905/SRX7399905.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7399905/SRX7399905.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 09:43:29: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:43:29: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:43:34: 1000000 INFO @ Wed, 22 Apr 2020 09:43:38: 2000000 INFO @ Wed, 22 Apr 2020 09:43:43: 3000000 INFO @ Wed, 22 Apr 2020 09:43:47: 4000000 INFO @ Wed, 22 Apr 2020 09:43:52: 5000000 INFO @ Wed, 22 Apr 2020 09:43:56: 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 09:43:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7399905/SRX7399905.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7399905/SRX7399905.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7399905/SRX7399905.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7399905/SRX7399905.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 09:43:59: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:43:59: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:44:01: 7000000 INFO @ Wed, 22 Apr 2020 09:44:04: 1000000 INFO @ Wed, 22 Apr 2020 09:44:06: 8000000 INFO @ Wed, 22 Apr 2020 09:44:09: 2000000 INFO @ Wed, 22 Apr 2020 09:44:11: 9000000 INFO @ Wed, 22 Apr 2020 09:44:14: 3000000 INFO @ Wed, 22 Apr 2020 09:44:16: 10000000 INFO @ Wed, 22 Apr 2020 09:44:19: 4000000 INFO @ Wed, 22 Apr 2020 09:44:21: 11000000 INFO @ Wed, 22 Apr 2020 09:44:24: 5000000 INFO @ Wed, 22 Apr 2020 09:44:26: 12000000 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 09:44:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7399905/SRX7399905.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7399905/SRX7399905.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7399905/SRX7399905.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7399905/SRX7399905.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 09:44:29: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:44:29: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:44:29: 6000000 INFO @ Wed, 22 Apr 2020 09:44:31: 13000000 INFO @ Wed, 22 Apr 2020 09:44:32: #1 tag size is determined as 41 bps INFO @ Wed, 22 Apr 2020 09:44:32: #1 tag size = 41 INFO @ Wed, 22 Apr 2020 09:44:32: #1 total tags in treatment: 1024923 INFO @ Wed, 22 Apr 2020 09:44:32: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:44:32: #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 09:44:32: #1 tags after filtering in treatment: 353138 INFO @ Wed, 22 Apr 2020 09:44:32: #1 Redundant rate of treatment: 0.66 INFO @ Wed, 22 Apr 2020 09:44:32: #1 finished! INFO @ Wed, 22 Apr 2020 09:44:32: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:44:32: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:44:32: #2 number of paired peaks: 501 WARNING @ Wed, 22 Apr 2020 09:44:32: Fewer paired peaks (501) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 501 pairs to build model! INFO @ Wed, 22 Apr 2020 09:44:32: start model_add_line... INFO @ Wed, 22 Apr 2020 09:44:32: start X-correlation... INFO @ Wed, 22 Apr 2020 09:44:32: end of X-cor INFO @ Wed, 22 Apr 2020 09:44:32: #2 finished! INFO @ Wed, 22 Apr 2020 09:44:32: #2 predicted fragment length is 205 bps INFO @ Wed, 22 Apr 2020 09:44:32: #2 alternative fragment length(s) may be 205 bps INFO @ Wed, 22 Apr 2020 09:44:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7399905/SRX7399905.05_model.r INFO @ Wed, 22 Apr 2020 09:44:32: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:44:32: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:44:33: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:44:34: 7000000 INFO @ Wed, 22 Apr 2020 09:44:34: 1000000 INFO @ Wed, 22 Apr 2020 09:44:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7399905/SRX7399905.05_peaks.xls INFO @ Wed, 22 Apr 2020 09:44:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7399905/SRX7399905.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:44:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7399905/SRX7399905.05_summits.bed INFO @ Wed, 22 Apr 2020 09:44:34: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (498 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:44:39: 8000000 INFO @ Wed, 22 Apr 2020 09:44:39: 2000000 INFO @ Wed, 22 Apr 2020 09:44:44: 9000000 INFO @ Wed, 22 Apr 2020 09:44:44: 3000000 INFO @ Wed, 22 Apr 2020 09:44:49: 10000000 INFO @ Wed, 22 Apr 2020 09:44:49: 4000000 INFO @ Wed, 22 Apr 2020 09:44:54: 11000000 INFO @ Wed, 22 Apr 2020 09:44:54: 5000000 INFO @ Wed, 22 Apr 2020 09:44:59: 12000000 INFO @ Wed, 22 Apr 2020 09:44:59: 6000000 INFO @ Wed, 22 Apr 2020 09:45:04: 7000000 INFO @ Wed, 22 Apr 2020 09:45:04: 13000000 INFO @ Wed, 22 Apr 2020 09:45:04: #1 tag size is determined as 41 bps INFO @ Wed, 22 Apr 2020 09:45:04: #1 tag size = 41 INFO @ Wed, 22 Apr 2020 09:45:04: #1 total tags in treatment: 1024923 INFO @ Wed, 22 Apr 2020 09:45:04: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:45:04: #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 09:45:04: #1 tags after filtering in treatment: 353138 INFO @ Wed, 22 Apr 2020 09:45:04: #1 Redundant rate of treatment: 0.66 INFO @ Wed, 22 Apr 2020 09:45:04: #1 finished! INFO @ Wed, 22 Apr 2020 09:45:04: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:45:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:45:04: #2 number of paired peaks: 501 WARNING @ Wed, 22 Apr 2020 09:45:04: Fewer paired peaks (501) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 501 pairs to build model! INFO @ Wed, 22 Apr 2020 09:45:04: start model_add_line... INFO @ Wed, 22 Apr 2020 09:45:04: start X-correlation... INFO @ Wed, 22 Apr 2020 09:45:04: end of X-cor INFO @ Wed, 22 Apr 2020 09:45:04: #2 finished! INFO @ Wed, 22 Apr 2020 09:45:04: #2 predicted fragment length is 205 bps INFO @ Wed, 22 Apr 2020 09:45:04: #2 alternative fragment length(s) may be 205 bps INFO @ Wed, 22 Apr 2020 09:45:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7399905/SRX7399905.10_model.r INFO @ Wed, 22 Apr 2020 09:45:04: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:45:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:45:06: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:45:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7399905/SRX7399905.10_peaks.xls INFO @ Wed, 22 Apr 2020 09:45:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7399905/SRX7399905.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:45:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7399905/SRX7399905.10_summits.bed INFO @ Wed, 22 Apr 2020 09:45:06: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (409 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:45:08: 8000000 INFO @ Wed, 22 Apr 2020 09:45:13: 9000000 INFO @ Wed, 22 Apr 2020 09:45:18: 10000000 INFO @ Wed, 22 Apr 2020 09:45:23: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:45:27: 12000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 09:45:32: 13000000 INFO @ Wed, 22 Apr 2020 09:45:33: #1 tag size is determined as 41 bps INFO @ Wed, 22 Apr 2020 09:45:33: #1 tag size = 41 INFO @ Wed, 22 Apr 2020 09:45:33: #1 total tags in treatment: 1024923 INFO @ Wed, 22 Apr 2020 09:45:33: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:45:33: #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 09:45:33: #1 tags after filtering in treatment: 353138 INFO @ Wed, 22 Apr 2020 09:45:33: #1 Redundant rate of treatment: 0.66 INFO @ Wed, 22 Apr 2020 09:45:33: #1 finished! INFO @ Wed, 22 Apr 2020 09:45:33: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:45:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:45:33: #2 number of paired peaks: 501 WARNING @ Wed, 22 Apr 2020 09:45:33: Fewer paired peaks (501) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 501 pairs to build model! INFO @ Wed, 22 Apr 2020 09:45:33: start model_add_line... INFO @ Wed, 22 Apr 2020 09:45:33: start X-correlation... INFO @ Wed, 22 Apr 2020 09:45:33: end of X-cor INFO @ Wed, 22 Apr 2020 09:45:33: #2 finished! INFO @ Wed, 22 Apr 2020 09:45:33: #2 predicted fragment length is 205 bps INFO @ Wed, 22 Apr 2020 09:45:33: #2 alternative fragment length(s) may be 205 bps INFO @ Wed, 22 Apr 2020 09:45:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7399905/SRX7399905.20_model.r INFO @ Wed, 22 Apr 2020 09:45:33: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:45:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:45:34: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:45:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7399905/SRX7399905.20_peaks.xls INFO @ Wed, 22 Apr 2020 09:45:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7399905/SRX7399905.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:45:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7399905/SRX7399905.20_summits.bed INFO @ Wed, 22 Apr 2020 09:45:35: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (346 records, 4 fields): 2 millis CompletedMACS2peakCalling