Job ID = 5790995 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,748,859 reads read : 3,497,718 reads written : 3,497,718 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: 00:01:30 1748859 reads; of these: 1748859 (100.00%) were paired; of these: 191877 (10.97%) aligned concordantly 0 times 1253372 (71.67%) aligned concordantly exactly 1 time 303610 (17.36%) aligned concordantly >1 times ---- 191877 pairs aligned concordantly 0 times; of these: 752 (0.39%) aligned discordantly 1 time ---- 191125 pairs aligned 0 times concordantly or discordantly; of these: 382250 mates make up the pairs; of these: 372648 (97.49%) aligned 0 times 5774 (1.51%) aligned exactly 1 time 3828 (1.00%) aligned >1 times 89.35% overall alignment rate Time searching: 00:01:30 Overall time: 00:01:30 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] 12629 / 1556067 = 0.0081 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 08:13:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874494/SRX5874494.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874494/SRX5874494.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874494/SRX5874494.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874494/SRX5874494.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 08:13:19: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:13:19: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:13:25: 1000000 INFO @ Wed, 22 Apr 2020 08:13:31: 2000000 INFO @ Wed, 22 Apr 2020 08:13:37: 3000000 INFO @ Wed, 22 Apr 2020 08:13:38: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:13:38: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:13:38: #1 total tags in treatment: 1544356 INFO @ Wed, 22 Apr 2020 08:13:38: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:13:38: #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 08:13:38: #1 tags after filtering in treatment: 1412141 INFO @ Wed, 22 Apr 2020 08:13:38: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 22 Apr 2020 08:13:38: #1 finished! INFO @ Wed, 22 Apr 2020 08:13:38: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:13:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:13:38: #2 number of paired peaks: 211 WARNING @ Wed, 22 Apr 2020 08:13:38: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Wed, 22 Apr 2020 08:13:38: start model_add_line... INFO @ Wed, 22 Apr 2020 08:13:38: start X-correlation... INFO @ Wed, 22 Apr 2020 08:13:38: end of X-cor INFO @ Wed, 22 Apr 2020 08:13:38: #2 finished! INFO @ Wed, 22 Apr 2020 08:13:38: #2 predicted fragment length is 146 bps INFO @ Wed, 22 Apr 2020 08:13:38: #2 alternative fragment length(s) may be 3,146,170 bps INFO @ Wed, 22 Apr 2020 08:13:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874494/SRX5874494.05_model.r WARNING @ Wed, 22 Apr 2020 08:13:38: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:13:38: #2 You may need to consider one of the other alternative d(s): 3,146,170 WARNING @ Wed, 22 Apr 2020 08:13:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 08:13:38: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:13:38: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:13:42: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:13:43: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874494/SRX5874494.05_peaks.xls INFO @ Wed, 22 Apr 2020 08:13:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874494/SRX5874494.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:13:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874494/SRX5874494.05_summits.bed INFO @ Wed, 22 Apr 2020 08:13:43: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (430 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 Apr 2020 08:13:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874494/SRX5874494.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874494/SRX5874494.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874494/SRX5874494.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874494/SRX5874494.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 08:13:49: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:13:49: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:13:56: 1000000 INFO @ Wed, 22 Apr 2020 08:14:01: 2000000 INFO @ Wed, 22 Apr 2020 08:14:07: 3000000 INFO @ Wed, 22 Apr 2020 08:14:07: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:14:07: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:14:07: #1 total tags in treatment: 1544356 INFO @ Wed, 22 Apr 2020 08:14:07: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:14:07: #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 08:14:07: #1 tags after filtering in treatment: 1412141 INFO @ Wed, 22 Apr 2020 08:14:07: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 22 Apr 2020 08:14:07: #1 finished! INFO @ Wed, 22 Apr 2020 08:14:07: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:14:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:14:07: #2 number of paired peaks: 211 WARNING @ Wed, 22 Apr 2020 08:14:07: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Wed, 22 Apr 2020 08:14:07: start model_add_line... INFO @ Wed, 22 Apr 2020 08:14:07: start X-correlation... INFO @ Wed, 22 Apr 2020 08:14:07: end of X-cor INFO @ Wed, 22 Apr 2020 08:14:07: #2 finished! INFO @ Wed, 22 Apr 2020 08:14:07: #2 predicted fragment length is 146 bps INFO @ Wed, 22 Apr 2020 08:14:07: #2 alternative fragment length(s) may be 3,146,170 bps INFO @ Wed, 22 Apr 2020 08:14:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874494/SRX5874494.10_model.r WARNING @ Wed, 22 Apr 2020 08:14:07: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:14:07: #2 You may need to consider one of the other alternative d(s): 3,146,170 WARNING @ Wed, 22 Apr 2020 08:14:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 08:14:07: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:14:07: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:14:11: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:14:13: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874494/SRX5874494.10_peaks.xls INFO @ Wed, 22 Apr 2020 08:14:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874494/SRX5874494.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:14:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874494/SRX5874494.10_summits.bed INFO @ Wed, 22 Apr 2020 08:14:13: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (245 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 Apr 2020 08:14:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874494/SRX5874494.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874494/SRX5874494.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874494/SRX5874494.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874494/SRX5874494.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 08:14:19: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:14:19: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:14:25: 1000000 INFO @ Wed, 22 Apr 2020 08:14:30: 2000000 INFO @ Wed, 22 Apr 2020 08:14:35: 3000000 INFO @ Wed, 22 Apr 2020 08:14:36: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:14:36: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:14:36: #1 total tags in treatment: 1544356 INFO @ Wed, 22 Apr 2020 08:14:36: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:14:36: #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 08:14:36: #1 tags after filtering in treatment: 1412141 INFO @ Wed, 22 Apr 2020 08:14:36: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 22 Apr 2020 08:14:36: #1 finished! INFO @ Wed, 22 Apr 2020 08:14:36: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:14:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:14:36: #2 number of paired peaks: 211 WARNING @ Wed, 22 Apr 2020 08:14:36: Fewer paired peaks (211) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 211 pairs to build model! INFO @ Wed, 22 Apr 2020 08:14:36: start model_add_line... INFO @ Wed, 22 Apr 2020 08:14:36: start X-correlation... INFO @ Wed, 22 Apr 2020 08:14:36: end of X-cor INFO @ Wed, 22 Apr 2020 08:14:36: #2 finished! INFO @ Wed, 22 Apr 2020 08:14:36: #2 predicted fragment length is 146 bps INFO @ Wed, 22 Apr 2020 08:14:36: #2 alternative fragment length(s) may be 3,146,170 bps INFO @ Wed, 22 Apr 2020 08:14:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874494/SRX5874494.20_model.r WARNING @ Wed, 22 Apr 2020 08:14:36: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:14:36: #2 You may need to consider one of the other alternative d(s): 3,146,170 WARNING @ Wed, 22 Apr 2020 08:14:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 08:14:36: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:14:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:14:40: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:14:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874494/SRX5874494.20_peaks.xls INFO @ Wed, 22 Apr 2020 08:14:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874494/SRX5874494.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:14:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874494/SRX5874494.20_summits.bed INFO @ Wed, 22 Apr 2020 08:14:41: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (103 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。