Job ID = 5790976 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 5,077,542 reads read : 10,155,084 reads written : 10,155,084 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: 00:03:43 5077542 reads; of these: 5077542 (100.00%) were paired; of these: 369127 (7.27%) aligned concordantly 0 times 3378191 (66.53%) aligned concordantly exactly 1 time 1330224 (26.20%) aligned concordantly >1 times ---- 369127 pairs aligned concordantly 0 times; of these: 19967 (5.41%) aligned discordantly 1 time ---- 349160 pairs aligned 0 times concordantly or discordantly; of these: 698320 mates make up the pairs; of these: 619528 (88.72%) aligned 0 times 40991 (5.87%) aligned exactly 1 time 37801 (5.41%) aligned >1 times 93.90% overall alignment rate Time searching: 00:03:43 Overall time: 00:03:43 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] 150154 / 4663767 = 0.0322 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 08:18:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874480/SRX5874480.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874480/SRX5874480.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874480/SRX5874480.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874480/SRX5874480.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 08:18:29: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:18:29: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:18:34: 1000000 INFO @ Wed, 22 Apr 2020 08:18:40: 2000000 INFO @ Wed, 22 Apr 2020 08:18:45: 3000000 INFO @ Wed, 22 Apr 2020 08:18:50: 4000000 INFO @ Wed, 22 Apr 2020 08:18:56: 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 08:18:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874480/SRX5874480.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874480/SRX5874480.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874480/SRX5874480.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874480/SRX5874480.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 08:18:59: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:18:59: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:19:01: 6000000 INFO @ Wed, 22 Apr 2020 08:19:05: 1000000 INFO @ Wed, 22 Apr 2020 08:19:07: 7000000 INFO @ Wed, 22 Apr 2020 08:19:10: 2000000 INFO @ Wed, 22 Apr 2020 08:19:13: 8000000 INFO @ Wed, 22 Apr 2020 08:19:16: 3000000 INFO @ Wed, 22 Apr 2020 08:19:19: 9000000 INFO @ Wed, 22 Apr 2020 08:19:20: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:19:20: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:19:20: #1 total tags in treatment: 4558290 INFO @ Wed, 22 Apr 2020 08:19:20: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:19:20: #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 08:19:20: #1 tags after filtering in treatment: 3377500 INFO @ Wed, 22 Apr 2020 08:19:20: #1 Redundant rate of treatment: 0.26 INFO @ Wed, 22 Apr 2020 08:19:20: #1 finished! INFO @ Wed, 22 Apr 2020 08:19:20: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:19:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:19:20: #2 number of paired peaks: 149 WARNING @ Wed, 22 Apr 2020 08:19:20: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Wed, 22 Apr 2020 08:19:20: start model_add_line... INFO @ Wed, 22 Apr 2020 08:19:20: start X-correlation... INFO @ Wed, 22 Apr 2020 08:19:20: end of X-cor INFO @ Wed, 22 Apr 2020 08:19:20: #2 finished! INFO @ Wed, 22 Apr 2020 08:19:20: #2 predicted fragment length is 114 bps INFO @ Wed, 22 Apr 2020 08:19:20: #2 alternative fragment length(s) may be 1,74,114,126,133,177,517 bps INFO @ Wed, 22 Apr 2020 08:19:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874480/SRX5874480.05_model.r WARNING @ Wed, 22 Apr 2020 08:19:20: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:19:20: #2 You may need to consider one of the other alternative d(s): 1,74,114,126,133,177,517 WARNING @ Wed, 22 Apr 2020 08:19:20: #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 08:19:20: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:19:20: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:19:22: 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 08:19:28: 5000000 INFO @ Wed, 22 Apr 2020 08:19:28: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:19:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874480/SRX5874480.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874480/SRX5874480.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874480/SRX5874480.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874480/SRX5874480.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 08:19:29: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:19:29: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:19:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874480/SRX5874480.05_peaks.xls INFO @ Wed, 22 Apr 2020 08:19:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874480/SRX5874480.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:19:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874480/SRX5874480.05_summits.bed INFO @ Wed, 22 Apr 2020 08:19:30: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (625 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:19:33: 6000000 INFO @ Wed, 22 Apr 2020 08:19:35: 1000000 INFO @ Wed, 22 Apr 2020 08:19:40: 7000000 INFO @ Wed, 22 Apr 2020 08:19:41: 2000000 INFO @ Wed, 22 Apr 2020 08:19:46: 8000000 INFO @ Wed, 22 Apr 2020 08:19:48: 3000000 INFO @ Wed, 22 Apr 2020 08:19:52: 9000000 INFO @ Wed, 22 Apr 2020 08:19:53: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:19:53: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:19:53: #1 total tags in treatment: 4558290 INFO @ Wed, 22 Apr 2020 08:19:53: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:19:53: #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 08:19:53: #1 tags after filtering in treatment: 3377500 INFO @ Wed, 22 Apr 2020 08:19:53: #1 Redundant rate of treatment: 0.26 INFO @ Wed, 22 Apr 2020 08:19:53: #1 finished! INFO @ Wed, 22 Apr 2020 08:19:53: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:19:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:19:53: #2 number of paired peaks: 149 WARNING @ Wed, 22 Apr 2020 08:19:53: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Wed, 22 Apr 2020 08:19:53: start model_add_line... INFO @ Wed, 22 Apr 2020 08:19:53: start X-correlation... INFO @ Wed, 22 Apr 2020 08:19:53: end of X-cor INFO @ Wed, 22 Apr 2020 08:19:53: #2 finished! INFO @ Wed, 22 Apr 2020 08:19:53: #2 predicted fragment length is 114 bps INFO @ Wed, 22 Apr 2020 08:19:53: #2 alternative fragment length(s) may be 1,74,114,126,133,177,517 bps INFO @ Wed, 22 Apr 2020 08:19:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874480/SRX5874480.10_model.r WARNING @ Wed, 22 Apr 2020 08:19:53: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:19:53: #2 You may need to consider one of the other alternative d(s): 1,74,114,126,133,177,517 WARNING @ Wed, 22 Apr 2020 08:19:53: #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 08:19:53: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:19:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:19:54: 4000000 INFO @ Wed, 22 Apr 2020 08:20:00: 5000000 INFO @ Wed, 22 Apr 2020 08:20:00: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:20:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874480/SRX5874480.10_peaks.xls INFO @ Wed, 22 Apr 2020 08:20:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874480/SRX5874480.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:20:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874480/SRX5874480.10_summits.bed INFO @ Wed, 22 Apr 2020 08:20:03: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (375 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:20:06: 6000000 INFO @ Wed, 22 Apr 2020 08:20:11: 7000000 INFO @ Wed, 22 Apr 2020 08:20:17: 8000000 INFO @ Wed, 22 Apr 2020 08:20:22: 9000000 INFO @ Wed, 22 Apr 2020 08:20:24: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:20:24: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:20:24: #1 total tags in treatment: 4558290 INFO @ Wed, 22 Apr 2020 08:20:24: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:20:24: #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 08:20:24: #1 tags after filtering in treatment: 3377500 INFO @ Wed, 22 Apr 2020 08:20:24: #1 Redundant rate of treatment: 0.26 INFO @ Wed, 22 Apr 2020 08:20:24: #1 finished! INFO @ Wed, 22 Apr 2020 08:20:24: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:20:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:20:24: #2 number of paired peaks: 149 WARNING @ Wed, 22 Apr 2020 08:20:24: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Wed, 22 Apr 2020 08:20:24: start model_add_line... INFO @ Wed, 22 Apr 2020 08:20:24: start X-correlation... INFO @ Wed, 22 Apr 2020 08:20:24: end of X-cor INFO @ Wed, 22 Apr 2020 08:20:24: #2 finished! INFO @ Wed, 22 Apr 2020 08:20:24: #2 predicted fragment length is 114 bps INFO @ Wed, 22 Apr 2020 08:20:24: #2 alternative fragment length(s) may be 1,74,114,126,133,177,517 bps INFO @ Wed, 22 Apr 2020 08:20:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874480/SRX5874480.20_model.r WARNING @ Wed, 22 Apr 2020 08:20:24: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:20:24: #2 You may need to consider one of the other alternative d(s): 1,74,114,126,133,177,517 WARNING @ Wed, 22 Apr 2020 08:20:24: #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 08:20:24: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:20:24: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 08:20:31: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:20:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874480/SRX5874480.20_peaks.xls INFO @ Wed, 22 Apr 2020 08:20:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874480/SRX5874480.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:20:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874480/SRX5874480.20_summits.bed INFO @ Wed, 22 Apr 2020 08:20:33: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (143 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。