Job ID = 5790847 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,894,414 reads read : 5,788,828 reads written : 5,788,828 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: 00:01:20 2894414 reads; of these: 2894414 (100.00%) were paired; of these: 61044 (2.11%) aligned concordantly 0 times 2486062 (85.89%) aligned concordantly exactly 1 time 347308 (12.00%) aligned concordantly >1 times ---- 61044 pairs aligned concordantly 0 times; of these: 3758 (6.16%) aligned discordantly 1 time ---- 57286 pairs aligned 0 times concordantly or discordantly; of these: 114572 mates make up the pairs; of these: 95089 (82.99%) aligned 0 times 15827 (13.81%) aligned exactly 1 time 3656 (3.19%) aligned >1 times 98.36% overall alignment rate Time searching: 00:01:20 Overall time: 00:01:20 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] 52397 / 2834052 = 0.0185 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 07:55:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5521496/SRX5521496.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5521496/SRX5521496.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5521496/SRX5521496.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5521496/SRX5521496.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 07:55:50: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:55:50: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:55:56: 1000000 INFO @ Wed, 22 Apr 2020 07:56:02: 2000000 INFO @ Wed, 22 Apr 2020 07:56:08: 3000000 INFO @ Wed, 22 Apr 2020 07:56:14: 4000000 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 07:56:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5521496/SRX5521496.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5521496/SRX5521496.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5521496/SRX5521496.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5521496/SRX5521496.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 07:56:20: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:56:20: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:56:21: 5000000 INFO @ Wed, 22 Apr 2020 07:56:24: #1 tag size is determined as 36 bps INFO @ Wed, 22 Apr 2020 07:56:24: #1 tag size = 36 INFO @ Wed, 22 Apr 2020 07:56:24: #1 total tags in treatment: 2781001 INFO @ Wed, 22 Apr 2020 07:56:24: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:56:24: #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 07:56:24: #1 tags after filtering in treatment: 2369231 INFO @ Wed, 22 Apr 2020 07:56:24: #1 Redundant rate of treatment: 0.15 INFO @ Wed, 22 Apr 2020 07:56:24: #1 finished! INFO @ Wed, 22 Apr 2020 07:56:24: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:56:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:56:24: #2 number of paired peaks: 145 WARNING @ Wed, 22 Apr 2020 07:56:24: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Wed, 22 Apr 2020 07:56:24: start model_add_line... INFO @ Wed, 22 Apr 2020 07:56:24: start X-correlation... INFO @ Wed, 22 Apr 2020 07:56:24: end of X-cor INFO @ Wed, 22 Apr 2020 07:56:24: #2 finished! INFO @ Wed, 22 Apr 2020 07:56:24: #2 predicted fragment length is 3 bps INFO @ Wed, 22 Apr 2020 07:56:24: #2 alternative fragment length(s) may be 3,17,55 bps INFO @ Wed, 22 Apr 2020 07:56:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5521496/SRX5521496.05_model.r WARNING @ Wed, 22 Apr 2020 07:56:24: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:56:24: #2 You may need to consider one of the other alternative d(s): 3,17,55 WARNING @ Wed, 22 Apr 2020 07:56:24: #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 07:56:24: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:56:24: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:56:27: 1000000 INFO @ Wed, 22 Apr 2020 07:56:28: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:56:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5521496/SRX5521496.05_peaks.xls INFO @ Wed, 22 Apr 2020 07:56:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5521496/SRX5521496.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:56:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5521496/SRX5521496.05_summits.bed INFO @ Wed, 22 Apr 2020 07:56:30: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 07:56:32: 2000000 INFO @ Wed, 22 Apr 2020 07:56:39: 3000000 INFO @ Wed, 22 Apr 2020 07:56:45: 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 07:56:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5521496/SRX5521496.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5521496/SRX5521496.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5521496/SRX5521496.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5521496/SRX5521496.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 07:56:50: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:56:50: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:56:51: 5000000 INFO @ Wed, 22 Apr 2020 07:56:54: #1 tag size is determined as 36 bps INFO @ Wed, 22 Apr 2020 07:56:54: #1 tag size = 36 INFO @ Wed, 22 Apr 2020 07:56:54: #1 total tags in treatment: 2781001 INFO @ Wed, 22 Apr 2020 07:56:54: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:56:54: #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 07:56:54: #1 tags after filtering in treatment: 2369231 INFO @ Wed, 22 Apr 2020 07:56:54: #1 Redundant rate of treatment: 0.15 INFO @ Wed, 22 Apr 2020 07:56:54: #1 finished! INFO @ Wed, 22 Apr 2020 07:56:54: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:56:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:56:54: #2 number of paired peaks: 145 WARNING @ Wed, 22 Apr 2020 07:56:54: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Wed, 22 Apr 2020 07:56:54: start model_add_line... INFO @ Wed, 22 Apr 2020 07:56:54: start X-correlation... INFO @ Wed, 22 Apr 2020 07:56:54: end of X-cor INFO @ Wed, 22 Apr 2020 07:56:54: #2 finished! INFO @ Wed, 22 Apr 2020 07:56:54: #2 predicted fragment length is 3 bps INFO @ Wed, 22 Apr 2020 07:56:54: #2 alternative fragment length(s) may be 3,17,55 bps INFO @ Wed, 22 Apr 2020 07:56:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5521496/SRX5521496.10_model.r WARNING @ Wed, 22 Apr 2020 07:56:54: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:56:54: #2 You may need to consider one of the other alternative d(s): 3,17,55 WARNING @ Wed, 22 Apr 2020 07:56:54: #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 07:56:54: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:56:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:56:57: 1000000 INFO @ Wed, 22 Apr 2020 07:56:58: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:57:00: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5521496/SRX5521496.10_peaks.xls INFO @ Wed, 22 Apr 2020 07:57:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5521496/SRX5521496.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:57:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5521496/SRX5521496.10_summits.bed INFO @ Wed, 22 Apr 2020 07:57:00: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 07:57:03: 2000000 INFO @ Wed, 22 Apr 2020 07:57:09: 3000000 INFO @ Wed, 22 Apr 2020 07:57:15: 4000000 INFO @ Wed, 22 Apr 2020 07:57:21: 5000000 INFO @ Wed, 22 Apr 2020 07:57:24: #1 tag size is determined as 36 bps INFO @ Wed, 22 Apr 2020 07:57:24: #1 tag size = 36 INFO @ Wed, 22 Apr 2020 07:57:24: #1 total tags in treatment: 2781001 INFO @ Wed, 22 Apr 2020 07:57:24: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:57:24: #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 07:57:24: #1 tags after filtering in treatment: 2369231 INFO @ Wed, 22 Apr 2020 07:57:24: #1 Redundant rate of treatment: 0.15 INFO @ Wed, 22 Apr 2020 07:57:24: #1 finished! INFO @ Wed, 22 Apr 2020 07:57:24: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:57:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:57:24: #2 number of paired peaks: 145 WARNING @ Wed, 22 Apr 2020 07:57:24: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Wed, 22 Apr 2020 07:57:24: start model_add_line... INFO @ Wed, 22 Apr 2020 07:57:24: start X-correlation... INFO @ Wed, 22 Apr 2020 07:57:24: end of X-cor INFO @ Wed, 22 Apr 2020 07:57:24: #2 finished! INFO @ Wed, 22 Apr 2020 07:57:24: #2 predicted fragment length is 3 bps INFO @ Wed, 22 Apr 2020 07:57:24: #2 alternative fragment length(s) may be 3,17,55 bps INFO @ Wed, 22 Apr 2020 07:57:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5521496/SRX5521496.20_model.r WARNING @ Wed, 22 Apr 2020 07:57:24: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:57:24: #2 You may need to consider one of the other alternative d(s): 3,17,55 WARNING @ Wed, 22 Apr 2020 07:57:24: #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 07:57:24: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:57:24: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:57:28: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 07:57:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5521496/SRX5521496.20_peaks.xls INFO @ Wed, 22 Apr 2020 07:57:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5521496/SRX5521496.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:57:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5521496/SRX5521496.20_summits.bed INFO @ Wed, 22 Apr 2020 07:57:29: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。