Job ID = 5791237 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 10,211,854 reads read : 20,423,708 reads written : 20,423,708 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: 00:06:21 10211854 reads; of these: 10211854 (100.00%) were paired; of these: 3524491 (34.51%) aligned concordantly 0 times 4022722 (39.39%) aligned concordantly exactly 1 time 2664641 (26.09%) aligned concordantly >1 times ---- 3524491 pairs aligned concordantly 0 times; of these: 8414 (0.24%) aligned discordantly 1 time ---- 3516077 pairs aligned 0 times concordantly or discordantly; of these: 7032154 mates make up the pairs; of these: 6853099 (97.45%) aligned 0 times 47022 (0.67%) aligned exactly 1 time 132033 (1.88%) aligned >1 times 66.45% overall alignment rate Time searching: 00:06:21 Overall time: 00:06:21 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_sort_core] merging from 8 files... [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] 2569043 / 6692535 = 0.3839 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 09:25:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7283195/SRX7283195.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7283195/SRX7283195.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7283195/SRX7283195.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7283195/SRX7283195.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 09:25:45: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:25:45: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:25:52: 1000000 INFO @ Wed, 22 Apr 2020 09:25:59: 2000000 INFO @ Wed, 22 Apr 2020 09:26:06: 3000000 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 09:26:13: 4000000 INFO @ Wed, 22 Apr 2020 09:26:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7283195/SRX7283195.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7283195/SRX7283195.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7283195/SRX7283195.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7283195/SRX7283195.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 09:26:14: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:26:14: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:26:21: 5000000 INFO @ Wed, 22 Apr 2020 09:26:22: 1000000 INFO @ Wed, 22 Apr 2020 09:26:29: 6000000 INFO @ Wed, 22 Apr 2020 09:26:30: 2000000 INFO @ Wed, 22 Apr 2020 09:26:37: 7000000 INFO @ Wed, 22 Apr 2020 09:26:38: 3000000 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 09:26:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7283195/SRX7283195.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7283195/SRX7283195.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7283195/SRX7283195.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7283195/SRX7283195.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 09:26:44: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:26:44: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:26:45: 8000000 INFO @ Wed, 22 Apr 2020 09:26:46: 4000000 INFO @ Wed, 22 Apr 2020 09:26:48: #1 tag size is determined as 76 bps INFO @ Wed, 22 Apr 2020 09:26:48: #1 tag size = 76 INFO @ Wed, 22 Apr 2020 09:26:48: #1 total tags in treatment: 4120526 INFO @ Wed, 22 Apr 2020 09:26:48: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:26:48: #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 09:26:48: #1 tags after filtering in treatment: 2250213 INFO @ Wed, 22 Apr 2020 09:26:48: #1 Redundant rate of treatment: 0.45 INFO @ Wed, 22 Apr 2020 09:26:48: #1 finished! INFO @ Wed, 22 Apr 2020 09:26:48: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:26:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:26:49: #2 number of paired peaks: 396 WARNING @ Wed, 22 Apr 2020 09:26:49: Fewer paired peaks (396) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 396 pairs to build model! INFO @ Wed, 22 Apr 2020 09:26:49: start model_add_line... INFO @ Wed, 22 Apr 2020 09:26:49: start X-correlation... INFO @ Wed, 22 Apr 2020 09:26:49: end of X-cor INFO @ Wed, 22 Apr 2020 09:26:49: #2 finished! INFO @ Wed, 22 Apr 2020 09:26:49: #2 predicted fragment length is 114 bps INFO @ Wed, 22 Apr 2020 09:26:49: #2 alternative fragment length(s) may be 3,114,126 bps INFO @ Wed, 22 Apr 2020 09:26:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7283195/SRX7283195.05_model.r WARNING @ Wed, 22 Apr 2020 09:26:49: #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 09:26:49: #2 You may need to consider one of the other alternative d(s): 3,114,126 WARNING @ Wed, 22 Apr 2020 09:26:49: #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 09:26:49: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:26:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:26:54: 1000000 INFO @ Wed, 22 Apr 2020 09:26:55: 5000000 INFO @ Wed, 22 Apr 2020 09:26:56: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:26:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7283195/SRX7283195.05_peaks.xls INFO @ Wed, 22 Apr 2020 09:26:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7283195/SRX7283195.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:26:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7283195/SRX7283195.05_summits.bed INFO @ Wed, 22 Apr 2020 09:26:58: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (1303 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 09:27:03: 6000000 INFO @ Wed, 22 Apr 2020 09:27:03: 2000000 INFO @ Wed, 22 Apr 2020 09:27:12: 7000000 INFO @ Wed, 22 Apr 2020 09:27:13: 3000000 INFO @ Wed, 22 Apr 2020 09:27:20: 8000000 INFO @ Wed, 22 Apr 2020 09:27:22: 4000000 INFO @ Wed, 22 Apr 2020 09:27:24: #1 tag size is determined as 76 bps INFO @ Wed, 22 Apr 2020 09:27:24: #1 tag size = 76 INFO @ Wed, 22 Apr 2020 09:27:24: #1 total tags in treatment: 4120526 INFO @ Wed, 22 Apr 2020 09:27:24: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:27:24: #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 09:27:24: #1 tags after filtering in treatment: 2250213 INFO @ Wed, 22 Apr 2020 09:27:24: #1 Redundant rate of treatment: 0.45 INFO @ Wed, 22 Apr 2020 09:27:24: #1 finished! INFO @ Wed, 22 Apr 2020 09:27:24: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:27:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:27:24: #2 number of paired peaks: 396 WARNING @ Wed, 22 Apr 2020 09:27:24: Fewer paired peaks (396) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 396 pairs to build model! INFO @ Wed, 22 Apr 2020 09:27:24: start model_add_line... INFO @ Wed, 22 Apr 2020 09:27:24: start X-correlation... INFO @ Wed, 22 Apr 2020 09:27:24: end of X-cor INFO @ Wed, 22 Apr 2020 09:27:24: #2 finished! INFO @ Wed, 22 Apr 2020 09:27:24: #2 predicted fragment length is 114 bps INFO @ Wed, 22 Apr 2020 09:27:24: #2 alternative fragment length(s) may be 3,114,126 bps INFO @ Wed, 22 Apr 2020 09:27:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7283195/SRX7283195.10_model.r WARNING @ Wed, 22 Apr 2020 09:27:24: #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 09:27:24: #2 You may need to consider one of the other alternative d(s): 3,114,126 WARNING @ Wed, 22 Apr 2020 09:27:24: #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 09:27:24: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:27:24: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:27:31: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:27:31: 5000000 INFO @ Wed, 22 Apr 2020 09:27:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7283195/SRX7283195.10_peaks.xls INFO @ Wed, 22 Apr 2020 09:27:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7283195/SRX7283195.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:27:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7283195/SRX7283195.10_summits.bed INFO @ Wed, 22 Apr 2020 09:27:33: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (996 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 09:27:40: 6000000 BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 09:27:49: 7000000 INFO @ Wed, 22 Apr 2020 09:27:57: 8000000 INFO @ Wed, 22 Apr 2020 09:28:01: #1 tag size is determined as 76 bps INFO @ Wed, 22 Apr 2020 09:28:01: #1 tag size = 76 INFO @ Wed, 22 Apr 2020 09:28:01: #1 total tags in treatment: 4120526 INFO @ Wed, 22 Apr 2020 09:28:01: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:28:01: #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 09:28:01: #1 tags after filtering in treatment: 2250213 INFO @ Wed, 22 Apr 2020 09:28:01: #1 Redundant rate of treatment: 0.45 INFO @ Wed, 22 Apr 2020 09:28:01: #1 finished! INFO @ Wed, 22 Apr 2020 09:28:01: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:28:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:28:01: #2 number of paired peaks: 396 WARNING @ Wed, 22 Apr 2020 09:28:01: Fewer paired peaks (396) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 396 pairs to build model! INFO @ Wed, 22 Apr 2020 09:28:01: start model_add_line... INFO @ Wed, 22 Apr 2020 09:28:01: start X-correlation... INFO @ Wed, 22 Apr 2020 09:28:01: end of X-cor INFO @ Wed, 22 Apr 2020 09:28:01: #2 finished! INFO @ Wed, 22 Apr 2020 09:28:01: #2 predicted fragment length is 114 bps INFO @ Wed, 22 Apr 2020 09:28:01: #2 alternative fragment length(s) may be 3,114,126 bps INFO @ Wed, 22 Apr 2020 09:28:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7283195/SRX7283195.20_model.r WARNING @ Wed, 22 Apr 2020 09:28:01: #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 09:28:01: #2 You may need to consider one of the other alternative d(s): 3,114,126 WARNING @ Wed, 22 Apr 2020 09:28:01: #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 09:28:01: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:28:01: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:28:08: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:28:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7283195/SRX7283195.20_peaks.xls INFO @ Wed, 22 Apr 2020 09:28:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7283195/SRX7283195.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:28:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7283195/SRX7283195.20_summits.bed INFO @ Wed, 22 Apr 2020 09:28:10: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (675 records, 4 fields): 3 millis CompletedMACS2peakCalling