Job ID = 10224109 SRX = SRX8952662 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5831739 spots for SRR12458224/SRR12458224.sra Written 5831739 spots for SRR12458224/SRR12458224.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: 00:11:23 5831739 reads; of these: 5831739 (100.00%) were paired; of these: 5073075 (86.99%) aligned concordantly 0 times 572959 (9.82%) aligned concordantly exactly 1 time 185705 (3.18%) aligned concordantly >1 times ---- 5073075 pairs aligned concordantly 0 times; of these: 2257 (0.04%) aligned discordantly 1 time ---- 5070818 pairs aligned 0 times concordantly or discordantly; of these: 10141636 mates make up the pairs; of these: 4849273 (47.82%) aligned 0 times 839535 (8.28%) aligned exactly 1 time 4452828 (43.91%) aligned >1 times 58.42% overall alignment rate Time searching: 00:11:23 Overall time: 00:11:23 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] 113241 / 758508 = 0.1493 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 @ Fri, 16 Oct 2020 09:39:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952662/SRX8952662.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952662/SRX8952662.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952662/SRX8952662.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952662/SRX8952662.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 @ Fri, 16 Oct 2020 09:39:33: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:39:33: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:39:37: 1000000 INFO @ Fri, 16 Oct 2020 09:39:41: 2000000 INFO @ Fri, 16 Oct 2020 09:39:45: 3000000 INFO @ Fri, 16 Oct 2020 09:39:48: 4000000 INFO @ Fri, 16 Oct 2020 09:39:52: 5000000 INFO @ Fri, 16 Oct 2020 09:39:56: 6000000 INFO @ Fri, 16 Oct 2020 09:39:58: #1 tag size is determined as 13 bps INFO @ Fri, 16 Oct 2020 09:39:58: #1 tag size = 13 INFO @ Fri, 16 Oct 2020 09:39:58: #1 total tags in treatment: 645429 INFO @ Fri, 16 Oct 2020 09:39:58: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:39:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 09:39:58: #1 tags after filtering in treatment: 571480 INFO @ Fri, 16 Oct 2020 09:39:58: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 16 Oct 2020 09:39:58: #1 finished! INFO @ Fri, 16 Oct 2020 09:39:58: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:39:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:39:58: #2 number of paired peaks: 209 WARNING @ Fri, 16 Oct 2020 09:39:58: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Fri, 16 Oct 2020 09:39:58: start model_add_line... INFO @ Fri, 16 Oct 2020 09:39:58: start X-correlation... INFO @ Fri, 16 Oct 2020 09:39:58: end of X-cor INFO @ Fri, 16 Oct 2020 09:39:58: #2 finished! INFO @ Fri, 16 Oct 2020 09:39:58: #2 predicted fragment length is 263 bps INFO @ Fri, 16 Oct 2020 09:39:58: #2 alternative fragment length(s) may be 1,72,146,225,244,263,298,500,585 bps INFO @ Fri, 16 Oct 2020 09:39:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952662/SRX8952662.05_model.r INFO @ Fri, 16 Oct 2020 09:39:58: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:39:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:40:00: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:40:00: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952662/SRX8952662.05_peaks.xls INFO @ Fri, 16 Oct 2020 09:40:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952662/SRX8952662.05_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:40:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952662/SRX8952662.05_summits.bed INFO @ Fri, 16 Oct 2020 09:40:01: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (113 records, 4 fields): 105 millis CompletedMACS2peakCalling 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 @ Fri, 16 Oct 2020 09:40:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952662/SRX8952662.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952662/SRX8952662.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952662/SRX8952662.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952662/SRX8952662.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 @ Fri, 16 Oct 2020 09:40:03: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:40:03: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:40:07: 1000000 INFO @ Fri, 16 Oct 2020 09:40:11: 2000000 INFO @ Fri, 16 Oct 2020 09:40:15: 3000000 INFO @ Fri, 16 Oct 2020 09:40:18: 4000000 INFO @ Fri, 16 Oct 2020 09:40:22: 5000000 INFO @ Fri, 16 Oct 2020 09:40:26: 6000000 INFO @ Fri, 16 Oct 2020 09:40:28: #1 tag size is determined as 13 bps INFO @ Fri, 16 Oct 2020 09:40:28: #1 tag size = 13 INFO @ Fri, 16 Oct 2020 09:40:28: #1 total tags in treatment: 645429 INFO @ Fri, 16 Oct 2020 09:40:28: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:40:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 09:40:28: #1 tags after filtering in treatment: 571480 INFO @ Fri, 16 Oct 2020 09:40:28: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 16 Oct 2020 09:40:28: #1 finished! INFO @ Fri, 16 Oct 2020 09:40:28: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:40:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:40:28: #2 number of paired peaks: 209 WARNING @ Fri, 16 Oct 2020 09:40:28: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Fri, 16 Oct 2020 09:40:28: start model_add_line... INFO @ Fri, 16 Oct 2020 09:40:28: start X-correlation... INFO @ Fri, 16 Oct 2020 09:40:28: end of X-cor INFO @ Fri, 16 Oct 2020 09:40:28: #2 finished! INFO @ Fri, 16 Oct 2020 09:40:28: #2 predicted fragment length is 263 bps INFO @ Fri, 16 Oct 2020 09:40:28: #2 alternative fragment length(s) may be 1,72,146,225,244,263,298,500,585 bps INFO @ Fri, 16 Oct 2020 09:40:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952662/SRX8952662.10_model.r INFO @ Fri, 16 Oct 2020 09:40:28: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:40:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:40:30: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:40:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952662/SRX8952662.10_peaks.xls INFO @ Fri, 16 Oct 2020 09:40:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952662/SRX8952662.10_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:40:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952662/SRX8952662.10_summits.bed INFO @ Fri, 16 Oct 2020 09:40:30: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (58 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 @ Fri, 16 Oct 2020 09:40:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8952662/SRX8952662.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8952662/SRX8952662.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8952662/SRX8952662.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8952662/SRX8952662.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 @ Fri, 16 Oct 2020 09:40:33: #1 read tag files... INFO @ Fri, 16 Oct 2020 09:40:33: #1 read treatment tags... INFO @ Fri, 16 Oct 2020 09:40:37: 1000000 INFO @ Fri, 16 Oct 2020 09:40:41: 2000000 INFO @ Fri, 16 Oct 2020 09:40:45: 3000000 INFO @ Fri, 16 Oct 2020 09:40:48: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 16 Oct 2020 09:40:52: 5000000 INFO @ Fri, 16 Oct 2020 09:40:56: 6000000 BigWig に変換しました。 INFO @ Fri, 16 Oct 2020 09:40:59: #1 tag size is determined as 13 bps INFO @ Fri, 16 Oct 2020 09:40:59: #1 tag size = 13 INFO @ Fri, 16 Oct 2020 09:40:59: #1 total tags in treatment: 645429 INFO @ Fri, 16 Oct 2020 09:40:59: #1 user defined the maximum tags... INFO @ Fri, 16 Oct 2020 09:40:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Oct 2020 09:40:59: #1 tags after filtering in treatment: 571480 INFO @ Fri, 16 Oct 2020 09:40:59: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 16 Oct 2020 09:40:59: #1 finished! INFO @ Fri, 16 Oct 2020 09:40:59: #2 Build Peak Model... INFO @ Fri, 16 Oct 2020 09:40:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Oct 2020 09:40:59: #2 number of paired peaks: 209 WARNING @ Fri, 16 Oct 2020 09:40:59: Fewer paired peaks (209) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 209 pairs to build model! INFO @ Fri, 16 Oct 2020 09:40:59: start model_add_line... INFO @ Fri, 16 Oct 2020 09:40:59: start X-correlation... INFO @ Fri, 16 Oct 2020 09:40:59: end of X-cor INFO @ Fri, 16 Oct 2020 09:40:59: #2 finished! INFO @ Fri, 16 Oct 2020 09:40:59: #2 predicted fragment length is 263 bps INFO @ Fri, 16 Oct 2020 09:40:59: #2 alternative fragment length(s) may be 1,72,146,225,244,263,298,500,585 bps INFO @ Fri, 16 Oct 2020 09:40:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8952662/SRX8952662.20_model.r INFO @ Fri, 16 Oct 2020 09:40:59: #3 Call peaks... INFO @ Fri, 16 Oct 2020 09:40:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Oct 2020 09:41:01: #3 Call peaks for each chromosome... INFO @ Fri, 16 Oct 2020 09:41:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8952662/SRX8952662.20_peaks.xls INFO @ Fri, 16 Oct 2020 09:41:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8952662/SRX8952662.20_peaks.narrowPeak INFO @ Fri, 16 Oct 2020 09:41:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8952662/SRX8952662.20_summits.bed INFO @ Fri, 16 Oct 2020 09:41:01: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (35 records, 4 fields): 1 millis CompletedMACS2peakCalling