Job ID = 5790979 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,101,140 reads read : 6,202,280 reads written : 6,202,280 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: 00:02:48 3101140 reads; of these: 3101140 (100.00%) were paired; of these: 282569 (9.11%) aligned concordantly 0 times 2152479 (69.41%) aligned concordantly exactly 1 time 666092 (21.48%) aligned concordantly >1 times ---- 282569 pairs aligned concordantly 0 times; of these: 9636 (3.41%) aligned discordantly 1 time ---- 272933 pairs aligned 0 times concordantly or discordantly; of these: 545866 mates make up the pairs; of these: 507846 (93.03%) aligned 0 times 21467 (3.93%) aligned exactly 1 time 16553 (3.03%) aligned >1 times 91.81% overall alignment rate Time searching: 00:02:48 Overall time: 00:02:48 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] 91243 / 2815527 = 0.0324 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 08:15:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874482/SRX5874482.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874482/SRX5874482.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874482/SRX5874482.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874482/SRX5874482.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 08:15:23: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:15:23: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:15:28: 1000000 INFO @ Wed, 22 Apr 2020 08:15:33: 2000000 INFO @ Wed, 22 Apr 2020 08:15:38: 3000000 INFO @ Wed, 22 Apr 2020 08:15:43: 4000000 INFO @ Wed, 22 Apr 2020 08:15:48: 5000000 INFO @ Wed, 22 Apr 2020 08:15:51: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:15:51: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:15:51: #1 total tags in treatment: 2727372 INFO @ Wed, 22 Apr 2020 08:15:51: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:15:51: #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 08:15:51: #1 tags after filtering in treatment: 2243429 INFO @ Wed, 22 Apr 2020 08:15:51: #1 Redundant rate of treatment: 0.18 INFO @ Wed, 22 Apr 2020 08:15:51: #1 finished! INFO @ Wed, 22 Apr 2020 08:15:51: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:15:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:15:51: #2 number of paired peaks: 175 WARNING @ Wed, 22 Apr 2020 08:15:51: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Wed, 22 Apr 2020 08:15:51: start model_add_line... INFO @ Wed, 22 Apr 2020 08:15:51: start X-correlation... INFO @ Wed, 22 Apr 2020 08:15:51: end of X-cor INFO @ Wed, 22 Apr 2020 08:15:51: #2 finished! INFO @ Wed, 22 Apr 2020 08:15:51: #2 predicted fragment length is 154 bps INFO @ Wed, 22 Apr 2020 08:15:51: #2 alternative fragment length(s) may be 2,73,94,123,125,154,188,217 bps INFO @ Wed, 22 Apr 2020 08:15:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874482/SRX5874482.05_model.r INFO @ Wed, 22 Apr 2020 08:15:51: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:15:51: #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 08:15:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874482/SRX5874482.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874482/SRX5874482.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874482/SRX5874482.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874482/SRX5874482.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 08:15:53: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:15:53: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:15:57: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:15:58: 1000000 INFO @ Wed, 22 Apr 2020 08:15:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874482/SRX5874482.05_peaks.xls INFO @ Wed, 22 Apr 2020 08:15:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874482/SRX5874482.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:15:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874482/SRX5874482.05_summits.bed INFO @ Wed, 22 Apr 2020 08:15:58: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (479 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:16:03: 2000000 INFO @ Wed, 22 Apr 2020 08:16:08: 3000000 INFO @ Wed, 22 Apr 2020 08:16:13: 4000000 INFO @ Wed, 22 Apr 2020 08:16:19: 5000000 INFO @ Wed, 22 Apr 2020 08:16:21: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:16:21: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:16:21: #1 total tags in treatment: 2727372 INFO @ Wed, 22 Apr 2020 08:16:21: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:16:21: #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 08:16:21: #1 tags after filtering in treatment: 2243429 INFO @ Wed, 22 Apr 2020 08:16:21: #1 Redundant rate of treatment: 0.18 INFO @ Wed, 22 Apr 2020 08:16:21: #1 finished! INFO @ Wed, 22 Apr 2020 08:16:21: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:16:21: #2 looking for paired plus/minus strand peaks... 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 08:16:21: #2 number of paired peaks: 175 WARNING @ Wed, 22 Apr 2020 08:16:21: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Wed, 22 Apr 2020 08:16:21: start model_add_line... INFO @ Wed, 22 Apr 2020 08:16:21: start X-correlation... INFO @ Wed, 22 Apr 2020 08:16:21: end of X-cor INFO @ Wed, 22 Apr 2020 08:16:21: #2 finished! INFO @ Wed, 22 Apr 2020 08:16:21: #2 predicted fragment length is 154 bps INFO @ Wed, 22 Apr 2020 08:16:21: #2 alternative fragment length(s) may be 2,73,94,123,125,154,188,217 bps INFO @ Wed, 22 Apr 2020 08:16:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874482/SRX5874482.10_model.r INFO @ Wed, 22 Apr 2020 08:16:21: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:16:21: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:16:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874482/SRX5874482.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874482/SRX5874482.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874482/SRX5874482.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874482/SRX5874482.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 08:16:23: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:16:23: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:16:27: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:16:28: 1000000 INFO @ Wed, 22 Apr 2020 08:16:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874482/SRX5874482.10_peaks.xls INFO @ Wed, 22 Apr 2020 08:16:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874482/SRX5874482.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:16:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874482/SRX5874482.10_summits.bed INFO @ Wed, 22 Apr 2020 08:16:29: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (275 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:16:34: 2000000 INFO @ Wed, 22 Apr 2020 08:16:39: 3000000 INFO @ Wed, 22 Apr 2020 08:16:44: 4000000 INFO @ Wed, 22 Apr 2020 08:16:50: 5000000 INFO @ Wed, 22 Apr 2020 08:16:52: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:16:52: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:16:52: #1 total tags in treatment: 2727372 INFO @ Wed, 22 Apr 2020 08:16:52: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:16:52: #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 08:16:52: #1 tags after filtering in treatment: 2243429 INFO @ Wed, 22 Apr 2020 08:16:52: #1 Redundant rate of treatment: 0.18 INFO @ Wed, 22 Apr 2020 08:16:52: #1 finished! INFO @ Wed, 22 Apr 2020 08:16:52: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:16:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:16:52: #2 number of paired peaks: 175 WARNING @ Wed, 22 Apr 2020 08:16:52: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Wed, 22 Apr 2020 08:16:52: start model_add_line... INFO @ Wed, 22 Apr 2020 08:16:52: start X-correlation... INFO @ Wed, 22 Apr 2020 08:16:52: end of X-cor INFO @ Wed, 22 Apr 2020 08:16:52: #2 finished! INFO @ Wed, 22 Apr 2020 08:16:52: #2 predicted fragment length is 154 bps INFO @ Wed, 22 Apr 2020 08:16:52: #2 alternative fragment length(s) may be 2,73,94,123,125,154,188,217 bps INFO @ Wed, 22 Apr 2020 08:16:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874482/SRX5874482.20_model.r INFO @ Wed, 22 Apr 2020 08:16:52: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:16:52: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:16:58: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:17:00: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874482/SRX5874482.20_peaks.xls INFO @ Wed, 22 Apr 2020 08:17:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874482/SRX5874482.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:17:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874482/SRX5874482.20_summits.bed INFO @ Wed, 22 Apr 2020 08:17:00: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (131 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。