Job ID = 5790959 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,735,852 reads read : 7,471,704 reads written : 7,471,704 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: 00:02:51 3735852 reads; of these: 3735852 (100.00%) were paired; of these: 177053 (4.74%) aligned concordantly 0 times 2680312 (71.75%) aligned concordantly exactly 1 time 878487 (23.52%) aligned concordantly >1 times ---- 177053 pairs aligned concordantly 0 times; of these: 4342 (2.45%) aligned discordantly 1 time ---- 172711 pairs aligned 0 times concordantly or discordantly; of these: 345422 mates make up the pairs; of these: 309446 (89.58%) aligned 0 times 20707 (5.99%) aligned exactly 1 time 15269 (4.42%) aligned >1 times 95.86% overall alignment rate Time searching: 00:02:51 Overall time: 00:02:51 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] 127191 / 3559680 = 0.0357 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 08:15:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874472/SRX5874472.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874472/SRX5874472.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874472/SRX5874472.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874472/SRX5874472.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 08:15:54: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:15:54: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:16:00: 1000000 INFO @ Wed, 22 Apr 2020 08:16:05: 2000000 INFO @ Wed, 22 Apr 2020 08:16:10: 3000000 INFO @ Wed, 22 Apr 2020 08:16:15: 4000000 INFO @ Wed, 22 Apr 2020 08:16:20: 5000000 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 08:16:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874472/SRX5874472.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874472/SRX5874472.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874472/SRX5874472.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874472/SRX5874472.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 08:16:24: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:16:24: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:16:26: 6000000 INFO @ Wed, 22 Apr 2020 08:16:30: 1000000 INFO @ Wed, 22 Apr 2020 08:16:31: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:16:31: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:16:31: #1 total tags in treatment: 3431624 INFO @ Wed, 22 Apr 2020 08:16:31: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:16:31: #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 08:16:31: #1 tags after filtering in treatment: 2752401 INFO @ Wed, 22 Apr 2020 08:16:31: #1 Redundant rate of treatment: 0.20 INFO @ Wed, 22 Apr 2020 08:16:31: #1 finished! INFO @ Wed, 22 Apr 2020 08:16:31: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:16:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:16:31: #2 number of paired peaks: 177 WARNING @ Wed, 22 Apr 2020 08:16:31: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Wed, 22 Apr 2020 08:16:31: start model_add_line... INFO @ Wed, 22 Apr 2020 08:16:31: start X-correlation... INFO @ Wed, 22 Apr 2020 08:16:31: end of X-cor INFO @ Wed, 22 Apr 2020 08:16:31: #2 finished! INFO @ Wed, 22 Apr 2020 08:16:31: #2 predicted fragment length is 137 bps INFO @ Wed, 22 Apr 2020 08:16:31: #2 alternative fragment length(s) may be 2,61,102,121,137,153,201 bps INFO @ Wed, 22 Apr 2020 08:16:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874472/SRX5874472.05_model.r WARNING @ Wed, 22 Apr 2020 08:16:31: #2 Since the d (137) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:16:31: #2 You may need to consider one of the other alternative d(s): 2,61,102,121,137,153,201 WARNING @ Wed, 22 Apr 2020 08:16:31: #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 08:16:31: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:16:31: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:16:36: 2000000 INFO @ Wed, 22 Apr 2020 08:16:37: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:16:40: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874472/SRX5874472.05_peaks.xls INFO @ Wed, 22 Apr 2020 08:16:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874472/SRX5874472.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:16:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874472/SRX5874472.05_summits.bed INFO @ Wed, 22 Apr 2020 08:16:40: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (554 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:16:42: 3000000 INFO @ Wed, 22 Apr 2020 08:16:48: 4000000 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 08:16:54: 5000000 INFO @ Wed, 22 Apr 2020 08:16:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874472/SRX5874472.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874472/SRX5874472.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874472/SRX5874472.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874472/SRX5874472.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 08:16:54: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:16:54: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:17:00: 1000000 INFO @ Wed, 22 Apr 2020 08:17:00: 6000000 INFO @ Wed, 22 Apr 2020 08:17:05: 2000000 INFO @ Wed, 22 Apr 2020 08:17:06: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:17:06: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:17:06: #1 total tags in treatment: 3431624 INFO @ Wed, 22 Apr 2020 08:17:06: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:17:06: #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 08:17:06: #1 tags after filtering in treatment: 2752401 INFO @ Wed, 22 Apr 2020 08:17:06: #1 Redundant rate of treatment: 0.20 INFO @ Wed, 22 Apr 2020 08:17:06: #1 finished! INFO @ Wed, 22 Apr 2020 08:17:06: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:17:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:17:06: #2 number of paired peaks: 177 WARNING @ Wed, 22 Apr 2020 08:17:06: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Wed, 22 Apr 2020 08:17:06: start model_add_line... INFO @ Wed, 22 Apr 2020 08:17:06: start X-correlation... INFO @ Wed, 22 Apr 2020 08:17:06: end of X-cor INFO @ Wed, 22 Apr 2020 08:17:06: #2 finished! INFO @ Wed, 22 Apr 2020 08:17:06: #2 predicted fragment length is 137 bps INFO @ Wed, 22 Apr 2020 08:17:06: #2 alternative fragment length(s) may be 2,61,102,121,137,153,201 bps INFO @ Wed, 22 Apr 2020 08:17:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874472/SRX5874472.10_model.r WARNING @ Wed, 22 Apr 2020 08:17:06: #2 Since the d (137) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:17:06: #2 You may need to consider one of the other alternative d(s): 2,61,102,121,137,153,201 WARNING @ Wed, 22 Apr 2020 08:17:06: #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 08:17:06: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:17:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:17:10: 3000000 INFO @ Wed, 22 Apr 2020 08:17:12: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:17:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874472/SRX5874472.10_peaks.xls INFO @ Wed, 22 Apr 2020 08:17:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874472/SRX5874472.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:17:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874472/SRX5874472.10_summits.bed INFO @ Wed, 22 Apr 2020 08:17:14: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (358 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:17:16: 4000000 INFO @ Wed, 22 Apr 2020 08:17:21: 5000000 INFO @ Wed, 22 Apr 2020 08:17:26: 6000000 INFO @ Wed, 22 Apr 2020 08:17:31: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:17:31: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:17:31: #1 total tags in treatment: 3431624 INFO @ Wed, 22 Apr 2020 08:17:31: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:17:31: #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 08:17:31: #1 tags after filtering in treatment: 2752401 INFO @ Wed, 22 Apr 2020 08:17:31: #1 Redundant rate of treatment: 0.20 INFO @ Wed, 22 Apr 2020 08:17:31: #1 finished! INFO @ Wed, 22 Apr 2020 08:17:31: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:17:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:17:31: #2 number of paired peaks: 177 WARNING @ Wed, 22 Apr 2020 08:17:31: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Wed, 22 Apr 2020 08:17:31: start model_add_line... INFO @ Wed, 22 Apr 2020 08:17:31: start X-correlation... INFO @ Wed, 22 Apr 2020 08:17:31: end of X-cor INFO @ Wed, 22 Apr 2020 08:17:31: #2 finished! INFO @ Wed, 22 Apr 2020 08:17:31: #2 predicted fragment length is 137 bps INFO @ Wed, 22 Apr 2020 08:17:31: #2 alternative fragment length(s) may be 2,61,102,121,137,153,201 bps INFO @ Wed, 22 Apr 2020 08:17:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874472/SRX5874472.20_model.r WARNING @ Wed, 22 Apr 2020 08:17:31: #2 Since the d (137) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:17:31: #2 You may need to consider one of the other alternative d(s): 2,61,102,121,137,153,201 WARNING @ Wed, 22 Apr 2020 08:17:31: #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 08:17:31: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:17:31: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:17:38: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:17:40: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874472/SRX5874472.20_peaks.xls INFO @ Wed, 22 Apr 2020 08:17:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874472/SRX5874472.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:17:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874472/SRX5874472.20_summits.bed INFO @ Wed, 22 Apr 2020 08:17:40: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (168 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。