Job ID = 14520997 SRX = SRX9158105 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9336549 spots for SRR12677940/SRR12677940.sra Written 9336549 spots for SRR12677940/SRR12677940.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: 00:06:42 9336549 reads; of these: 9336549 (100.00%) were paired; of these: 2086808 (22.35%) aligned concordantly 0 times 4677836 (50.10%) aligned concordantly exactly 1 time 2571905 (27.55%) aligned concordantly >1 times ---- 2086808 pairs aligned concordantly 0 times; of these: 15428 (0.74%) aligned discordantly 1 time ---- 2071380 pairs aligned 0 times concordantly or discordantly; of these: 4142760 mates make up the pairs; of these: 4074637 (98.36%) aligned 0 times 40354 (0.97%) aligned exactly 1 time 27769 (0.67%) aligned >1 times 78.18% overall alignment rate Time searching: 00:06:42 Overall time: 00:06:42 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 8 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] 3151292 / 7264399 = 0.4338 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 20:24:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9158105/SRX9158105.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9158105/SRX9158105.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9158105/SRX9158105.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9158105/SRX9158105.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 20:24:51: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:24:51: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:24:56: 1000000 INFO @ Sat, 15 Jan 2022 20:25:01: 2000000 INFO @ Sat, 15 Jan 2022 20:25:06: 3000000 INFO @ Sat, 15 Jan 2022 20:25:11: 4000000 INFO @ Sat, 15 Jan 2022 20:25:16: 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 20:25:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9158105/SRX9158105.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9158105/SRX9158105.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9158105/SRX9158105.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9158105/SRX9158105.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 20:25:21: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:25:21: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:25:21: 6000000 INFO @ Sat, 15 Jan 2022 20:25:26: 1000000 INFO @ Sat, 15 Jan 2022 20:25:27: 7000000 INFO @ Sat, 15 Jan 2022 20:25:32: 8000000 INFO @ Sat, 15 Jan 2022 20:25:32: 2000000 INFO @ Sat, 15 Jan 2022 20:25:34: #1 tag size is determined as 42 bps INFO @ Sat, 15 Jan 2022 20:25:34: #1 tag size = 42 INFO @ Sat, 15 Jan 2022 20:25:34: #1 total tags in treatment: 4111394 INFO @ Sat, 15 Jan 2022 20:25:34: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:25:34: #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 20:25:34: #1 tags after filtering in treatment: 2268258 INFO @ Sat, 15 Jan 2022 20:25:34: #1 Redundant rate of treatment: 0.45 INFO @ Sat, 15 Jan 2022 20:25:34: #1 finished! INFO @ Sat, 15 Jan 2022 20:25:34: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:25:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:25:34: #2 number of paired peaks: 318 WARNING @ Sat, 15 Jan 2022 20:25:34: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Sat, 15 Jan 2022 20:25:34: start model_add_line... INFO @ Sat, 15 Jan 2022 20:25:34: start X-correlation... INFO @ Sat, 15 Jan 2022 20:25:34: end of X-cor INFO @ Sat, 15 Jan 2022 20:25:34: #2 finished! INFO @ Sat, 15 Jan 2022 20:25:34: #2 predicted fragment length is 329 bps INFO @ Sat, 15 Jan 2022 20:25:34: #2 alternative fragment length(s) may be 312,329 bps INFO @ Sat, 15 Jan 2022 20:25:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9158105/SRX9158105.05_model.r INFO @ Sat, 15 Jan 2022 20:25:34: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:25:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:25:37: 3000000 INFO @ Sat, 15 Jan 2022 20:25:42: 4000000 INFO @ Sat, 15 Jan 2022 20:25:48: 5000000 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 20:25:49: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:25:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX9158105/SRX9158105.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX9158105/SRX9158105.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX9158105/SRX9158105.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX9158105/SRX9158105.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 20:25:51: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:25:51: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:25:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9158105/SRX9158105.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:25:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9158105/SRX9158105.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:25:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9158105/SRX9158105.05_summits.bed INFO @ Sat, 15 Jan 2022 20:25:52: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (796 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:25:53: 6000000 INFO @ Sat, 15 Jan 2022 20:25:56: 1000000 INFO @ Sat, 15 Jan 2022 20:25:58: 7000000 INFO @ Sat, 15 Jan 2022 20:26:02: 2000000 INFO @ Sat, 15 Jan 2022 20:26:04: 8000000 INFO @ Sat, 15 Jan 2022 20:26:05: #1 tag size is determined as 42 bps INFO @ Sat, 15 Jan 2022 20:26:05: #1 tag size = 42 INFO @ Sat, 15 Jan 2022 20:26:05: #1 total tags in treatment: 4111394 INFO @ Sat, 15 Jan 2022 20:26:05: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:26:05: #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 20:26:05: #1 tags after filtering in treatment: 2268258 INFO @ Sat, 15 Jan 2022 20:26:05: #1 Redundant rate of treatment: 0.45 INFO @ Sat, 15 Jan 2022 20:26:05: #1 finished! INFO @ Sat, 15 Jan 2022 20:26:05: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:26:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:26:06: #2 number of paired peaks: 318 WARNING @ Sat, 15 Jan 2022 20:26:06: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Sat, 15 Jan 2022 20:26:06: start model_add_line... INFO @ Sat, 15 Jan 2022 20:26:06: start X-correlation... INFO @ Sat, 15 Jan 2022 20:26:06: end of X-cor INFO @ Sat, 15 Jan 2022 20:26:06: #2 finished! INFO @ Sat, 15 Jan 2022 20:26:06: #2 predicted fragment length is 329 bps INFO @ Sat, 15 Jan 2022 20:26:06: #2 alternative fragment length(s) may be 312,329 bps INFO @ Sat, 15 Jan 2022 20:26:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9158105/SRX9158105.10_model.r INFO @ Sat, 15 Jan 2022 20:26:06: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:26:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:26:07: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:26:12: 4000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:26:17: 5000000 INFO @ Sat, 15 Jan 2022 20:26:22: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:26:22: 6000000 INFO @ Sat, 15 Jan 2022 20:26:24: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9158105/SRX9158105.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:26:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9158105/SRX9158105.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:26:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9158105/SRX9158105.10_summits.bed INFO @ Sat, 15 Jan 2022 20:26:24: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (730 records, 4 fields): 231 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:26:27: 7000000 INFO @ Sat, 15 Jan 2022 20:26:32: 8000000 INFO @ Sat, 15 Jan 2022 20:26:34: #1 tag size is determined as 42 bps INFO @ Sat, 15 Jan 2022 20:26:34: #1 tag size = 42 INFO @ Sat, 15 Jan 2022 20:26:34: #1 total tags in treatment: 4111394 INFO @ Sat, 15 Jan 2022 20:26:34: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:26:34: #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 20:26:34: #1 tags after filtering in treatment: 2268258 INFO @ Sat, 15 Jan 2022 20:26:34: #1 Redundant rate of treatment: 0.45 INFO @ Sat, 15 Jan 2022 20:26:34: #1 finished! INFO @ Sat, 15 Jan 2022 20:26:34: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:26:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:26:34: #2 number of paired peaks: 318 WARNING @ Sat, 15 Jan 2022 20:26:34: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Sat, 15 Jan 2022 20:26:34: start model_add_line... INFO @ Sat, 15 Jan 2022 20:26:34: start X-correlation... INFO @ Sat, 15 Jan 2022 20:26:34: end of X-cor INFO @ Sat, 15 Jan 2022 20:26:34: #2 finished! INFO @ Sat, 15 Jan 2022 20:26:34: #2 predicted fragment length is 329 bps INFO @ Sat, 15 Jan 2022 20:26:34: #2 alternative fragment length(s) may be 312,329 bps INFO @ Sat, 15 Jan 2022 20:26:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX9158105/SRX9158105.20_model.r INFO @ Sat, 15 Jan 2022 20:26:34: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:26:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:26:50: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:26:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX9158105/SRX9158105.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:26:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX9158105/SRX9158105.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:26:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX9158105/SRX9158105.20_summits.bed INFO @ Sat, 15 Jan 2022 20:26:52: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (556 records, 4 fields): 2 millis CompletedMACS2peakCalling