Job ID = 14520440 SRX = SRX11781145 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2022-01-15T10:06:36 prefetch.2.10.7: 1) Downloading 'SRR15481088'... 2022-01-15T10:06:36 prefetch.2.10.7: Downloading via HTTPS... 2022-01-15T10:06:52 prefetch.2.10.7: HTTPS download succeed 2022-01-15T10:06:52 prefetch.2.10.7: 'SRR15481088' is valid 2022-01-15T10:06:52 prefetch.2.10.7: 1) 'SRR15481088' was downloaded successfully 2022-01-15T10:06:52 prefetch.2.10.7: 'SRR15481088' has 0 unresolved dependencies Read 6647787 spots for SRR15481088/SRR15481088.sra Written 6647787 spots for SRR15481088/SRR15481088.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: 00:02:39 6647787 reads; of these: 6647787 (100.00%) were paired; of these: 4144847 (62.35%) aligned concordantly 0 times 2181522 (32.82%) aligned concordantly exactly 1 time 321418 (4.83%) aligned concordantly >1 times ---- 4144847 pairs aligned concordantly 0 times; of these: 46561 (1.12%) aligned discordantly 1 time ---- 4098286 pairs aligned 0 times concordantly or discordantly; of these: 8196572 mates make up the pairs; of these: 4505075 (54.96%) aligned 0 times 3194140 (38.97%) aligned exactly 1 time 497357 (6.07%) aligned >1 times 66.12% overall alignment rate Time searching: 00:02:39 Overall time: 00:02:39 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] 245103 / 2548597 = 0.0962 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 19:12:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781145/SRX11781145.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781145/SRX11781145.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781145/SRX11781145.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781145/SRX11781145.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 19:12:21: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:12:21: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:12:26: 1000000 INFO @ Sat, 15 Jan 2022 19:12:31: 2000000 INFO @ Sat, 15 Jan 2022 19:12:36: 3000000 INFO @ Sat, 15 Jan 2022 19:12:41: 4000000 INFO @ Sat, 15 Jan 2022 19:12:46: 5000000 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 19:12:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781145/SRX11781145.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781145/SRX11781145.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781145/SRX11781145.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781145/SRX11781145.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 19:12:50: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:12:50: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:12:51: 6000000 INFO @ Sat, 15 Jan 2022 19:12:56: 1000000 INFO @ Sat, 15 Jan 2022 19:12:57: 7000000 INFO @ Sat, 15 Jan 2022 19:13:01: 2000000 INFO @ Sat, 15 Jan 2022 19:13:02: 8000000 INFO @ Sat, 15 Jan 2022 19:13:04: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:13:04: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:13:04: #1 total tags in treatment: 2260197 INFO @ Sat, 15 Jan 2022 19:13:04: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:13:04: #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 19:13:04: #1 tags after filtering in treatment: 1701960 INFO @ Sat, 15 Jan 2022 19:13:04: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 19:13:04: #1 finished! INFO @ Sat, 15 Jan 2022 19:13:04: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:13:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:13:04: #2 number of paired peaks: 182 WARNING @ Sat, 15 Jan 2022 19:13:04: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Sat, 15 Jan 2022 19:13:04: start model_add_line... INFO @ Sat, 15 Jan 2022 19:13:04: start X-correlation... INFO @ Sat, 15 Jan 2022 19:13:04: end of X-cor INFO @ Sat, 15 Jan 2022 19:13:04: #2 finished! INFO @ Sat, 15 Jan 2022 19:13:04: #2 predicted fragment length is 243 bps INFO @ Sat, 15 Jan 2022 19:13:04: #2 alternative fragment length(s) may be 1,217,243,258,262 bps INFO @ Sat, 15 Jan 2022 19:13:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781145/SRX11781145.05_model.r INFO @ Sat, 15 Jan 2022 19:13:04: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:13:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:13:06: 3000000 INFO @ Sat, 15 Jan 2022 19:13:08: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:13:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781145/SRX11781145.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:13:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781145/SRX11781145.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:13:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781145/SRX11781145.05_summits.bed INFO @ Sat, 15 Jan 2022 19:13:10: Done! INFO @ Sat, 15 Jan 2022 19:13:10: 4000000 pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (28 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:13:14: 5000000 INFO @ Sat, 15 Jan 2022 19:13:18: 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 19:13:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX11781145/SRX11781145.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX11781145/SRX11781145.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX11781145/SRX11781145.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX11781145/SRX11781145.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 19:13:20: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:13:20: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:13:23: 7000000 INFO @ Sat, 15 Jan 2022 19:13:26: 1000000 INFO @ Sat, 15 Jan 2022 19:13:28: 8000000 INFO @ Sat, 15 Jan 2022 19:13:29: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:13:29: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:13:29: #1 total tags in treatment: 2260197 INFO @ Sat, 15 Jan 2022 19:13:29: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:13:29: #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 19:13:29: #1 tags after filtering in treatment: 1701960 INFO @ Sat, 15 Jan 2022 19:13:29: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 19:13:29: #1 finished! INFO @ Sat, 15 Jan 2022 19:13:29: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:13:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:13:30: #2 number of paired peaks: 182 WARNING @ Sat, 15 Jan 2022 19:13:30: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Sat, 15 Jan 2022 19:13:30: start model_add_line... INFO @ Sat, 15 Jan 2022 19:13:30: start X-correlation... INFO @ Sat, 15 Jan 2022 19:13:30: end of X-cor INFO @ Sat, 15 Jan 2022 19:13:30: #2 finished! INFO @ Sat, 15 Jan 2022 19:13:30: #2 predicted fragment length is 243 bps INFO @ Sat, 15 Jan 2022 19:13:30: #2 alternative fragment length(s) may be 1,217,243,258,262 bps INFO @ Sat, 15 Jan 2022 19:13:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781145/SRX11781145.10_model.r INFO @ Sat, 15 Jan 2022 19:13:30: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:13:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:13:32: 2000000 INFO @ Sat, 15 Jan 2022 19:13:34: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:13:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781145/SRX11781145.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:13:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781145/SRX11781145.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:13:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781145/SRX11781145.10_summits.bed INFO @ Sat, 15 Jan 2022 19:13:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (14 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 19:13:37: 3000000 INFO @ Sat, 15 Jan 2022 19:13:42: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:13:47: 5000000 INFO @ Sat, 15 Jan 2022 19:13:53: 6000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:13:58: 7000000 INFO @ Sat, 15 Jan 2022 19:14:04: 8000000 INFO @ Sat, 15 Jan 2022 19:14:05: #1 tag size is determined as 38 bps INFO @ Sat, 15 Jan 2022 19:14:05: #1 tag size = 38 INFO @ Sat, 15 Jan 2022 19:14:05: #1 total tags in treatment: 2260197 INFO @ Sat, 15 Jan 2022 19:14:05: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:14:05: #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 19:14:05: #1 tags after filtering in treatment: 1701960 INFO @ Sat, 15 Jan 2022 19:14:05: #1 Redundant rate of treatment: 0.25 INFO @ Sat, 15 Jan 2022 19:14:05: #1 finished! INFO @ Sat, 15 Jan 2022 19:14:05: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:14:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:14:05: #2 number of paired peaks: 182 WARNING @ Sat, 15 Jan 2022 19:14:05: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Sat, 15 Jan 2022 19:14:05: start model_add_line... INFO @ Sat, 15 Jan 2022 19:14:05: start X-correlation... INFO @ Sat, 15 Jan 2022 19:14:05: end of X-cor INFO @ Sat, 15 Jan 2022 19:14:05: #2 finished! INFO @ Sat, 15 Jan 2022 19:14:05: #2 predicted fragment length is 243 bps INFO @ Sat, 15 Jan 2022 19:14:05: #2 alternative fragment length(s) may be 1,217,243,258,262 bps INFO @ Sat, 15 Jan 2022 19:14:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX11781145/SRX11781145.20_model.r INFO @ Sat, 15 Jan 2022 19:14:05: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:14:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:14:09: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:14:11: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX11781145/SRX11781145.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:14:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX11781145/SRX11781145.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:14:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX11781145/SRX11781145.20_summits.bed INFO @ Sat, 15 Jan 2022 19:14:11: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (7 records, 4 fields): 2 millis CompletedMACS2peakCalling