Job ID = 14520622 SRX = SRX11781088 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:27:32 prefetch.2.10.7: 1) Downloading 'SRR15481031'... 2022-01-15T10:27:32 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:28:45 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:28:45 prefetch.2.10.7: 1) 'SRR15481031' was downloaded successfully 2022-01-15T10:28:45 prefetch.2.10.7: 'SRR15481031' has 0 unresolved dependencies Read 18911511 spots for SRR15481031/SRR15481031.sra Written 18911511 spots for SRR15481031/SRR15481031.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: 00:57:44 18911511 reads; of these: 18911511 (100.00%) were paired; of these: 7544279 (39.89%) aligned concordantly 0 times 3898879 (20.62%) aligned concordantly exactly 1 time 7468353 (39.49%) aligned concordantly >1 times ---- 7544279 pairs aligned concordantly 0 times; of these: 37925 (0.50%) aligned discordantly 1 time ---- 7506354 pairs aligned 0 times concordantly or discordantly; of these: 15012708 mates make up the pairs; of these: 8514798 (56.72%) aligned 0 times 2263065 (15.07%) aligned exactly 1 time 4234845 (28.21%) aligned >1 times 77.49% overall alignment rate Time searching: 00:57:44 Overall time: 00:57:44 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 12 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] 1681064 / 11404191 = 0.1474 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 20:41:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781088/SRX11781088.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781088/SRX11781088.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781088/SRX11781088.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781088/SRX11781088.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 @ Sat, 15 Jan 2022 20:41:04: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:41:04: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:41:09: 1000000 INFO @ Sat, 15 Jan 2022 20:41:14: 2000000 INFO @ Sat, 15 Jan 2022 20:41:18: 3000000 INFO @ Sat, 15 Jan 2022 20:41:23: 4000000 INFO @ Sat, 15 Jan 2022 20:41:27: 5000000 INFO @ Sat, 15 Jan 2022 20:41:32: 6000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 20:41:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781088/SRX11781088.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781088/SRX11781088.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781088/SRX11781088.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781088/SRX11781088.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 @ Sat, 15 Jan 2022 20:41:34: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:41:34: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:41:37: 7000000 INFO @ Sat, 15 Jan 2022 20:41:39: 1000000 INFO @ Sat, 15 Jan 2022 20:41:41: 8000000 INFO @ Sat, 15 Jan 2022 20:41:44: 2000000 INFO @ Sat, 15 Jan 2022 20:41:46: 9000000 INFO @ Sat, 15 Jan 2022 20:41:48: 3000000 INFO @ Sat, 15 Jan 2022 20:41:51: 10000000 INFO @ Sat, 15 Jan 2022 20:41:53: 4000000 INFO @ Sat, 15 Jan 2022 20:41:55: 11000000 INFO @ Sat, 15 Jan 2022 20:41:57: 5000000 INFO @ Sat, 15 Jan 2022 20:42:00: 12000000 INFO @ Sat, 15 Jan 2022 20:42:02: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 20:42:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781088/SRX11781088.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781088/SRX11781088.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781088/SRX11781088.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781088/SRX11781088.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 @ Sat, 15 Jan 2022 20:42:04: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:42:04: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:42:04: 13000000 INFO @ Sat, 15 Jan 2022 20:42:07: 7000000 INFO @ Sat, 15 Jan 2022 20:42:09: 14000000 INFO @ Sat, 15 Jan 2022 20:42:10: 1000000 INFO @ Sat, 15 Jan 2022 20:42:11: 8000000 INFO @ Sat, 15 Jan 2022 20:42:14: 15000000 INFO @ Sat, 15 Jan 2022 20:42:15: 2000000 INFO @ Sat, 15 Jan 2022 20:42:16: 9000000 INFO @ Sat, 15 Jan 2022 20:42:19: 16000000 INFO @ Sat, 15 Jan 2022 20:42:21: 10000000 INFO @ Sat, 15 Jan 2022 20:42:21: 3000000 INFO @ Sat, 15 Jan 2022 20:42:23: 17000000 INFO @ Sat, 15 Jan 2022 20:42:25: 11000000 INFO @ Sat, 15 Jan 2022 20:42:27: 4000000 INFO @ Sat, 15 Jan 2022 20:42:28: 18000000 INFO @ Sat, 15 Jan 2022 20:42:30: 12000000 INFO @ Sat, 15 Jan 2022 20:42:33: 5000000 INFO @ Sat, 15 Jan 2022 20:42:33: 19000000 INFO @ Sat, 15 Jan 2022 20:42:35: 13000000 INFO @ Sat, 15 Jan 2022 20:42:37: 20000000 INFO @ Sat, 15 Jan 2022 20:42:38: 6000000 INFO @ Sat, 15 Jan 2022 20:42:39: 14000000 INFO @ Sat, 15 Jan 2022 20:42:42: 21000000 INFO @ Sat, 15 Jan 2022 20:42:44: 15000000 INFO @ Sat, 15 Jan 2022 20:42:44: 7000000 INFO @ Sat, 15 Jan 2022 20:42:47: 22000000 INFO @ Sat, 15 Jan 2022 20:42:49: 16000000 INFO @ Sat, 15 Jan 2022 20:42:49: 8000000 INFO @ Sat, 15 Jan 2022 20:42:52: 23000000 INFO @ Sat, 15 Jan 2022 20:42:53: 17000000 INFO @ Sat, 15 Jan 2022 20:42:54: 9000000 INFO @ Sat, 15 Jan 2022 20:42:56: 24000000 INFO @ Sat, 15 Jan 2022 20:42:58: 18000000 INFO @ Sat, 15 Jan 2022 20:43:00: 10000000 INFO @ Sat, 15 Jan 2022 20:43:01: 25000000 INFO @ Sat, 15 Jan 2022 20:43:03: 19000000 INFO @ Sat, 15 Jan 2022 20:43:05: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 20:43:05: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 20:43:05: #1 total tags in treatment: 9687914 INFO @ Sat, 15 Jan 2022 20:43:05: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:43:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 20:43:06: #1 tags after filtering in treatment: 3392387 INFO @ Sat, 15 Jan 2022 20:43:06: #1 Redundant rate of treatment: 0.65 INFO @ Sat, 15 Jan 2022 20:43:06: #1 finished! INFO @ Sat, 15 Jan 2022 20:43:06: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:43:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:43:06: 11000000 INFO @ Sat, 15 Jan 2022 20:43:06: #2 number of paired peaks: 143 WARNING @ Sat, 15 Jan 2022 20:43:06: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Sat, 15 Jan 2022 20:43:06: start model_add_line... INFO @ Sat, 15 Jan 2022 20:43:06: start X-correlation... INFO @ Sat, 15 Jan 2022 20:43:06: end of X-cor INFO @ Sat, 15 Jan 2022 20:43:06: #2 finished! INFO @ Sat, 15 Jan 2022 20:43:06: #2 predicted fragment length is 168 bps INFO @ Sat, 15 Jan 2022 20:43:06: #2 alternative fragment length(s) may be 0,168,194,216,237,266 bps INFO @ Sat, 15 Jan 2022 20:43:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781088/SRX11781088.05_model.r INFO @ Sat, 15 Jan 2022 20:43:06: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:43:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:43:08: 20000000 INFO @ Sat, 15 Jan 2022 20:43:12: 12000000 INFO @ Sat, 15 Jan 2022 20:43:13: 21000000 INFO @ Sat, 15 Jan 2022 20:43:14: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:43:17: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781088/SRX11781088.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:43:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781088/SRX11781088.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:43:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781088/SRX11781088.05_summits.bed INFO @ Sat, 15 Jan 2022 20:43:17: Done! INFO @ Sat, 15 Jan 2022 20:43:17: 22000000 INFO @ Sat, 15 Jan 2022 20:43:17: 13000000 pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (461 records, 4 fields): 1052 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:43:22: 23000000 INFO @ Sat, 15 Jan 2022 20:43:23: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:43:27: 24000000 INFO @ Sat, 15 Jan 2022 20:43:29: 15000000 INFO @ Sat, 15 Jan 2022 20:43:32: 25000000 INFO @ Sat, 15 Jan 2022 20:43:34: 16000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:43:36: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 20:43:36: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 20:43:36: #1 total tags in treatment: 9687914 INFO @ Sat, 15 Jan 2022 20:43:36: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:43:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 20:43:36: #1 tags after filtering in treatment: 3392387 INFO @ Sat, 15 Jan 2022 20:43:36: #1 Redundant rate of treatment: 0.65 INFO @ Sat, 15 Jan 2022 20:43:36: #1 finished! INFO @ Sat, 15 Jan 2022 20:43:36: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:43:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:43:37: #2 number of paired peaks: 143 WARNING @ Sat, 15 Jan 2022 20:43:37: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Sat, 15 Jan 2022 20:43:37: start model_add_line... INFO @ Sat, 15 Jan 2022 20:43:37: start X-correlation... INFO @ Sat, 15 Jan 2022 20:43:37: end of X-cor INFO @ Sat, 15 Jan 2022 20:43:37: #2 finished! INFO @ Sat, 15 Jan 2022 20:43:37: #2 predicted fragment length is 168 bps INFO @ Sat, 15 Jan 2022 20:43:37: #2 alternative fragment length(s) may be 0,168,194,216,237,266 bps INFO @ Sat, 15 Jan 2022 20:43:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781088/SRX11781088.10_model.r INFO @ Sat, 15 Jan 2022 20:43:37: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:43:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:43:39: 17000000 INFO @ Sat, 15 Jan 2022 20:43:45: 18000000 INFO @ Sat, 15 Jan 2022 20:43:45: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:43:48: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781088/SRX11781088.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:43:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781088/SRX11781088.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:43:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781088/SRX11781088.10_summits.bed INFO @ Sat, 15 Jan 2022 20:43:48: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (212 records, 4 fields): 222 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:43:50: 19000000 INFO @ Sat, 15 Jan 2022 20:43:55: 20000000 INFO @ Sat, 15 Jan 2022 20:44:01: 21000000 INFO @ Sat, 15 Jan 2022 20:44:06: 22000000 INFO @ Sat, 15 Jan 2022 20:44:12: 23000000 INFO @ Sat, 15 Jan 2022 20:44:17: 24000000 INFO @ Sat, 15 Jan 2022 20:44:23: 25000000 INFO @ Sat, 15 Jan 2022 20:44:29: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 20:44:29: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 20:44:29: #1 total tags in treatment: 9687914 INFO @ Sat, 15 Jan 2022 20:44:29: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:44:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 20:44:29: #1 tags after filtering in treatment: 3392387 INFO @ Sat, 15 Jan 2022 20:44:29: #1 Redundant rate of treatment: 0.65 INFO @ Sat, 15 Jan 2022 20:44:29: #1 finished! INFO @ Sat, 15 Jan 2022 20:44:29: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:44:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:44:29: #2 number of paired peaks: 143 WARNING @ Sat, 15 Jan 2022 20:44:29: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Sat, 15 Jan 2022 20:44:29: start model_add_line... INFO @ Sat, 15 Jan 2022 20:44:29: start X-correlation... INFO @ Sat, 15 Jan 2022 20:44:29: end of X-cor INFO @ Sat, 15 Jan 2022 20:44:29: #2 finished! INFO @ Sat, 15 Jan 2022 20:44:29: #2 predicted fragment length is 168 bps INFO @ Sat, 15 Jan 2022 20:44:29: #2 alternative fragment length(s) may be 0,168,194,216,237,266 bps INFO @ Sat, 15 Jan 2022 20:44:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781088/SRX11781088.20_model.r INFO @ Sat, 15 Jan 2022 20:44:29: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:44:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:44:37: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:44:39: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781088/SRX11781088.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:44:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781088/SRX11781088.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:44:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781088/SRX11781088.20_summits.bed INFO @ Sat, 15 Jan 2022 20:44:40: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (60 records, 4 fields): 79 millis CompletedMACS2peakCalling