Job ID = 7118081 SRX = SRX8639575 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-22T07:10:16 prefetch.2.10.7: 1) Downloading 'SRR12117013'... 2020-07-22T07:10:16 prefetch.2.10.7: Downloading via HTTPS... 2020-07-22T07:11:51 prefetch.2.10.7: HTTPS download succeed 2020-07-22T07:11:52 prefetch.2.10.7: 'SRR12117013' is valid 2020-07-22T07:11:52 prefetch.2.10.7: 1) 'SRR12117013' was downloaded successfully 2020-07-22T07:11:52 prefetch.2.10.7: 'SRR12117013' has 0 unresolved dependencies Read 15254330 spots for SRR12117013/SRR12117013.sra Written 15254330 spots for SRR12117013/SRR12117013.sra 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: 00:02:48 15254330 reads; of these: 15254330 (100.00%) were paired; of these: 12550397 (82.27%) aligned concordantly 0 times 2394927 (15.70%) aligned concordantly exactly 1 time 309006 (2.03%) aligned concordantly >1 times ---- 12550397 pairs aligned concordantly 0 times; of these: 31989 (0.25%) aligned discordantly 1 time ---- 12518408 pairs aligned 0 times concordantly or discordantly; of these: 25036816 mates make up the pairs; of these: 24993156 (99.83%) aligned 0 times 26577 (0.11%) aligned exactly 1 time 17083 (0.07%) aligned >1 times 18.08% overall alignment rate Time searching: 00:02:48 Overall time: 00:02:48 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] 22214 / 2735002 = 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 Jul 2020 16:17:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639575/SRX8639575.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639575/SRX8639575.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639575/SRX8639575.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639575/SRX8639575.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 Jul 2020 16:17:32: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:17:32: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:17:36: 1000000 INFO @ Wed, 22 Jul 2020 16:17:41: 2000000 INFO @ Wed, 22 Jul 2020 16:17:45: 3000000 INFO @ Wed, 22 Jul 2020 16:17:50: 4000000 INFO @ Wed, 22 Jul 2020 16:17:54: 5000000 INFO @ Wed, 22 Jul 2020 16:17:57: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:17:57: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:17:57: #1 total tags in treatment: 2681733 INFO @ Wed, 22 Jul 2020 16:17:57: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:17:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 16:17:57: #1 tags after filtering in treatment: 2370253 INFO @ Wed, 22 Jul 2020 16:17:57: #1 Redundant rate of treatment: 0.12 INFO @ Wed, 22 Jul 2020 16:17:57: #1 finished! INFO @ Wed, 22 Jul 2020 16:17:57: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:17:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:17:57: #2 number of paired peaks: 100 WARNING @ Wed, 22 Jul 2020 16:17:57: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Wed, 22 Jul 2020 16:17:57: start model_add_line... INFO @ Wed, 22 Jul 2020 16:17:57: start X-correlation... INFO @ Wed, 22 Jul 2020 16:17:57: end of X-cor INFO @ Wed, 22 Jul 2020 16:17:57: #2 finished! INFO @ Wed, 22 Jul 2020 16:17:57: #2 predicted fragment length is 74 bps INFO @ Wed, 22 Jul 2020 16:17:57: #2 alternative fragment length(s) may be 2,74,119,149,165,191,208 bps INFO @ Wed, 22 Jul 2020 16:17:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8639575/SRX8639575.05_model.r WARNING @ Wed, 22 Jul 2020 16:17:57: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 16:17:57: #2 You may need to consider one of the other alternative d(s): 2,74,119,149,165,191,208 WARNING @ Wed, 22 Jul 2020 16:17:57: #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 Jul 2020 16:17:57: #3 Call peaks... INFO @ Wed, 22 Jul 2020 16:17:57: #3 Pre-compute pvalue-qvalue table... 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 Jul 2020 16:18:01: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 16:18:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639575/SRX8639575.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639575/SRX8639575.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639575/SRX8639575.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639575/SRX8639575.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 Jul 2020 16:18:02: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:18:02: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:18:04: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8639575/SRX8639575.05_peaks.xls INFO @ Wed, 22 Jul 2020 16:18:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8639575/SRX8639575.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 16:18:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8639575/SRX8639575.05_summits.bed INFO @ Wed, 22 Jul 2020 16:18:04: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1393 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:18:07: 1000000 INFO @ Wed, 22 Jul 2020 16:18:12: 2000000 INFO @ Wed, 22 Jul 2020 16:18:17: 3000000 INFO @ Wed, 22 Jul 2020 16:18:22: 4000000 INFO @ Wed, 22 Jul 2020 16:18:27: 5000000 INFO @ Wed, 22 Jul 2020 16:18:29: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:18:29: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:18:29: #1 total tags in treatment: 2681733 INFO @ Wed, 22 Jul 2020 16:18:29: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:18:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 16:18:29: #1 tags after filtering in treatment: 2370253 INFO @ Wed, 22 Jul 2020 16:18:29: #1 Redundant rate of treatment: 0.12 INFO @ Wed, 22 Jul 2020 16:18:29: #1 finished! INFO @ Wed, 22 Jul 2020 16:18:29: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:18:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:18:29: #2 number of paired peaks: 100 WARNING @ Wed, 22 Jul 2020 16:18:29: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Wed, 22 Jul 2020 16:18:29: start model_add_line... INFO @ Wed, 22 Jul 2020 16:18:29: start X-correlation... INFO @ Wed, 22 Jul 2020 16:18:29: end of X-cor INFO @ Wed, 22 Jul 2020 16:18:29: #2 finished! INFO @ Wed, 22 Jul 2020 16:18:29: #2 predicted fragment length is 74 bps INFO @ Wed, 22 Jul 2020 16:18:29: #2 alternative fragment length(s) may be 2,74,119,149,165,191,208 bps INFO @ Wed, 22 Jul 2020 16:18:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8639575/SRX8639575.10_model.r WARNING @ Wed, 22 Jul 2020 16:18:29: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 16:18:29: #2 You may need to consider one of the other alternative d(s): 2,74,119,149,165,191,208 WARNING @ Wed, 22 Jul 2020 16:18:29: #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 Jul 2020 16:18:29: #3 Call peaks... INFO @ Wed, 22 Jul 2020 16:18:29: #3 Pre-compute pvalue-qvalue table... 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 Jul 2020 16:18:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8639575/SRX8639575.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8639575/SRX8639575.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8639575/SRX8639575.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8639575/SRX8639575.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 Jul 2020 16:18:31: #1 read tag files... INFO @ Wed, 22 Jul 2020 16:18:31: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 16:18:34: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 16:18:36: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8639575/SRX8639575.10_peaks.xls INFO @ Wed, 22 Jul 2020 16:18:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8639575/SRX8639575.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 16:18:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8639575/SRX8639575.10_summits.bed INFO @ Wed, 22 Jul 2020 16:18:36: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (621 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 16:18:36: 1000000 INFO @ Wed, 22 Jul 2020 16:18:41: 2000000 INFO @ Wed, 22 Jul 2020 16:18:45: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 16:18:50: 4000000 INFO @ Wed, 22 Jul 2020 16:18:54: 5000000 INFO @ Wed, 22 Jul 2020 16:18:56: #1 tag size is determined as 50 bps INFO @ Wed, 22 Jul 2020 16:18:56: #1 tag size = 50 INFO @ Wed, 22 Jul 2020 16:18:56: #1 total tags in treatment: 2681733 INFO @ Wed, 22 Jul 2020 16:18:56: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 16:18:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 16:18:56: #1 tags after filtering in treatment: 2370253 INFO @ Wed, 22 Jul 2020 16:18:56: #1 Redundant rate of treatment: 0.12 INFO @ Wed, 22 Jul 2020 16:18:56: #1 finished! INFO @ Wed, 22 Jul 2020 16:18:56: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 16:18:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 16:18:57: #2 number of paired peaks: 100 WARNING @ Wed, 22 Jul 2020 16:18:57: Fewer paired peaks (100) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 100 pairs to build model! INFO @ Wed, 22 Jul 2020 16:18:57: start model_add_line... INFO @ Wed, 22 Jul 2020 16:18:57: start X-correlation... INFO @ Wed, 22 Jul 2020 16:18:57: end of X-cor INFO @ Wed, 22 Jul 2020 16:18:57: #2 finished! INFO @ Wed, 22 Jul 2020 16:18:57: #2 predicted fragment length is 74 bps INFO @ Wed, 22 Jul 2020 16:18:57: #2 alternative fragment length(s) may be 2,74,119,149,165,191,208 bps INFO @ Wed, 22 Jul 2020 16:18:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8639575/SRX8639575.20_model.r WARNING @ Wed, 22 Jul 2020 16:18:57: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 16:18:57: #2 You may need to consider one of the other alternative d(s): 2,74,119,149,165,191,208 WARNING @ Wed, 22 Jul 2020 16:18:57: #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 Jul 2020 16:18:57: #3 Call peaks... INFO @ Wed, 22 Jul 2020 16:18:57: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 16:19:01: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 16:19:03: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8639575/SRX8639575.20_peaks.xls INFO @ Wed, 22 Jul 2020 16:19:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8639575/SRX8639575.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 16:19:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8639575/SRX8639575.20_summits.bed INFO @ Wed, 22 Jul 2020 16:19:03: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (109 records, 4 fields): 2 millis CompletedMACS2peakCalling