Job ID = 5791257 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 4,824,877 reads read : 9,649,754 reads written : 9,649,754 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: 00:02:09 4824877 reads; of these: 4824877 (100.00%) were paired; of these: 360972 (7.48%) aligned concordantly 0 times 3766887 (78.07%) aligned concordantly exactly 1 time 697018 (14.45%) aligned concordantly >1 times ---- 360972 pairs aligned concordantly 0 times; of these: 60698 (16.82%) aligned discordantly 1 time ---- 300274 pairs aligned 0 times concordantly or discordantly; of these: 600548 mates make up the pairs; of these: 491379 (81.82%) aligned 0 times 68491 (11.40%) aligned exactly 1 time 40678 (6.77%) aligned >1 times 94.91% overall alignment rate Time searching: 00:02:09 Overall time: 00:02:09 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] 1123456 / 4491245 = 0.2501 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 09:17:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388398/SRX7388398.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388398/SRX7388398.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388398/SRX7388398.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388398/SRX7388398.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 09:17:58: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:17:58: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:18:03: 1000000 INFO @ Wed, 22 Apr 2020 09:18:07: 2000000 INFO @ Wed, 22 Apr 2020 09:18:12: 3000000 INFO @ Wed, 22 Apr 2020 09:18:16: 4000000 INFO @ Wed, 22 Apr 2020 09:18:21: 5000000 INFO @ Wed, 22 Apr 2020 09:18:25: 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 09:18:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388398/SRX7388398.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388398/SRX7388398.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388398/SRX7388398.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388398/SRX7388398.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 09:18:28: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:18:28: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:18:29: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:18:29: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:18:29: #1 total tags in treatment: 3342547 INFO @ Wed, 22 Apr 2020 09:18:29: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:18:29: #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 09:18:29: #1 tags after filtering in treatment: 2084967 INFO @ Wed, 22 Apr 2020 09:18:29: #1 Redundant rate of treatment: 0.38 INFO @ Wed, 22 Apr 2020 09:18:29: #1 finished! INFO @ Wed, 22 Apr 2020 09:18:29: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:18:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:18:29: #2 number of paired peaks: 125 WARNING @ Wed, 22 Apr 2020 09:18:29: Fewer paired peaks (125) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 125 pairs to build model! INFO @ Wed, 22 Apr 2020 09:18:29: start model_add_line... INFO @ Wed, 22 Apr 2020 09:18:29: start X-correlation... INFO @ Wed, 22 Apr 2020 09:18:29: end of X-cor INFO @ Wed, 22 Apr 2020 09:18:29: #2 finished! INFO @ Wed, 22 Apr 2020 09:18:29: #2 predicted fragment length is 67 bps INFO @ Wed, 22 Apr 2020 09:18:29: #2 alternative fragment length(s) may be 1,32,35,67 bps INFO @ Wed, 22 Apr 2020 09:18:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388398/SRX7388398.05_model.r INFO @ Wed, 22 Apr 2020 09:18:29: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:18:29: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:18:33: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:18:33: 1000000 INFO @ Wed, 22 Apr 2020 09:18:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388398/SRX7388398.05_peaks.xls INFO @ Wed, 22 Apr 2020 09:18:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388398/SRX7388398.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:18:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388398/SRX7388398.05_summits.bed INFO @ Wed, 22 Apr 2020 09:18:35: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1811 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:18:38: 2000000 INFO @ Wed, 22 Apr 2020 09:18:44: 3000000 INFO @ Wed, 22 Apr 2020 09:18:49: 4000000 INFO @ Wed, 22 Apr 2020 09:18:54: 5000000 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 09:18:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7388398/SRX7388398.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7388398/SRX7388398.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7388398/SRX7388398.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7388398/SRX7388398.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 09:18:58: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:18:58: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:18:59: 6000000 INFO @ Wed, 22 Apr 2020 09:19:03: 1000000 INFO @ Wed, 22 Apr 2020 09:19:04: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:19:04: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:19:04: #1 total tags in treatment: 3342547 INFO @ Wed, 22 Apr 2020 09:19:04: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:19:04: #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 09:19:04: #1 tags after filtering in treatment: 2084967 INFO @ Wed, 22 Apr 2020 09:19:04: #1 Redundant rate of treatment: 0.38 INFO @ Wed, 22 Apr 2020 09:19:04: #1 finished! INFO @ Wed, 22 Apr 2020 09:19:04: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:19:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:19:04: #2 number of paired peaks: 125 WARNING @ Wed, 22 Apr 2020 09:19:04: Fewer paired peaks (125) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 125 pairs to build model! INFO @ Wed, 22 Apr 2020 09:19:04: start model_add_line... INFO @ Wed, 22 Apr 2020 09:19:04: start X-correlation... INFO @ Wed, 22 Apr 2020 09:19:04: end of X-cor INFO @ Wed, 22 Apr 2020 09:19:04: #2 finished! INFO @ Wed, 22 Apr 2020 09:19:04: #2 predicted fragment length is 67 bps INFO @ Wed, 22 Apr 2020 09:19:04: #2 alternative fragment length(s) may be 1,32,35,67 bps INFO @ Wed, 22 Apr 2020 09:19:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388398/SRX7388398.10_model.r INFO @ Wed, 22 Apr 2020 09:19:04: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:19:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:19:08: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:19:08: 2000000 INFO @ Wed, 22 Apr 2020 09:19:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388398/SRX7388398.10_peaks.xls INFO @ Wed, 22 Apr 2020 09:19:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388398/SRX7388398.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:19:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388398/SRX7388398.10_summits.bed INFO @ Wed, 22 Apr 2020 09:19:09: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (993 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:19:13: 3000000 INFO @ Wed, 22 Apr 2020 09:19:17: 4000000 INFO @ Wed, 22 Apr 2020 09:19:22: 5000000 INFO @ Wed, 22 Apr 2020 09:19:26: 6000000 INFO @ Wed, 22 Apr 2020 09:19:30: #1 tag size is determined as 25 bps INFO @ Wed, 22 Apr 2020 09:19:30: #1 tag size = 25 INFO @ Wed, 22 Apr 2020 09:19:30: #1 total tags in treatment: 3342547 INFO @ Wed, 22 Apr 2020 09:19:30: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:19:30: #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 09:19:30: #1 tags after filtering in treatment: 2084967 INFO @ Wed, 22 Apr 2020 09:19:30: #1 Redundant rate of treatment: 0.38 INFO @ Wed, 22 Apr 2020 09:19:30: #1 finished! INFO @ Wed, 22 Apr 2020 09:19:30: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:19:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:19:31: #2 number of paired peaks: 125 WARNING @ Wed, 22 Apr 2020 09:19:31: Fewer paired peaks (125) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 125 pairs to build model! INFO @ Wed, 22 Apr 2020 09:19:31: start model_add_line... INFO @ Wed, 22 Apr 2020 09:19:31: start X-correlation... INFO @ Wed, 22 Apr 2020 09:19:31: end of X-cor INFO @ Wed, 22 Apr 2020 09:19:31: #2 finished! INFO @ Wed, 22 Apr 2020 09:19:31: #2 predicted fragment length is 67 bps INFO @ Wed, 22 Apr 2020 09:19:31: #2 alternative fragment length(s) may be 1,32,35,67 bps INFO @ Wed, 22 Apr 2020 09:19:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7388398/SRX7388398.20_model.r INFO @ Wed, 22 Apr 2020 09:19:31: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:19:31: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:19:35: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:19:37: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7388398/SRX7388398.20_peaks.xls INFO @ Wed, 22 Apr 2020 09:19:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7388398/SRX7388398.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:19:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7388398/SRX7388398.20_summits.bed INFO @ Wed, 22 Apr 2020 09:19:37: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (262 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。