Job ID = 14520330 SRX = SRX8398386 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 1696340 spots for SRR11848078/SRR11848078.sra Written 1696340 spots for SRR11848078/SRR11848078.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: 00:01:10 1696340 reads; of these: 1696340 (100.00%) were paired; of these: 250940 (14.79%) aligned concordantly 0 times 1306532 (77.02%) aligned concordantly exactly 1 time 138868 (8.19%) aligned concordantly >1 times ---- 250940 pairs aligned concordantly 0 times; of these: 17098 (6.81%) aligned discordantly 1 time ---- 233842 pairs aligned 0 times concordantly or discordantly; of these: 467684 mates make up the pairs; of these: 454910 (97.27%) aligned 0 times 8228 (1.76%) aligned exactly 1 time 4546 (0.97%) aligned >1 times 86.59% overall alignment rate Time searching: 00:01:10 Overall time: 00:01:10 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] 85840 / 1462336 = 0.0587 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 18:59:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8398386/SRX8398386.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8398386/SRX8398386.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8398386/SRX8398386.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8398386/SRX8398386.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 18:59:57: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:59:57: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:00:04: 1000000 INFO @ Sat, 15 Jan 2022 19:00:10: 2000000 INFO @ Sat, 15 Jan 2022 19:00:15: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 19:00:15: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 19:00:15: #1 total tags in treatment: 1359871 INFO @ Sat, 15 Jan 2022 19:00:15: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:00:15: #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 19:00:16: #1 tags after filtering in treatment: 1067869 INFO @ Sat, 15 Jan 2022 19:00:16: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Jan 2022 19:00:16: #1 finished! INFO @ Sat, 15 Jan 2022 19:00:16: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:00:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:00:16: #2 number of paired peaks: 135 WARNING @ Sat, 15 Jan 2022 19:00:16: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Sat, 15 Jan 2022 19:00:16: start model_add_line... INFO @ Sat, 15 Jan 2022 19:00:16: start X-correlation... INFO @ Sat, 15 Jan 2022 19:00:16: end of X-cor INFO @ Sat, 15 Jan 2022 19:00:16: #2 finished! INFO @ Sat, 15 Jan 2022 19:00:16: #2 predicted fragment length is 106 bps INFO @ Sat, 15 Jan 2022 19:00:16: #2 alternative fragment length(s) may be 9,60,74,106,153,186,248,382 bps INFO @ Sat, 15 Jan 2022 19:00:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8398386/SRX8398386.05_model.r INFO @ Sat, 15 Jan 2022 19:00:16: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:00:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:00:18: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:00:20: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8398386/SRX8398386.05_peaks.xls INFO @ Sat, 15 Jan 2022 19:00:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8398386/SRX8398386.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:00:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8398386/SRX8398386.05_summits.bed INFO @ Sat, 15 Jan 2022 19:00:20: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (183 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 19:00:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8398386/SRX8398386.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8398386/SRX8398386.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8398386/SRX8398386.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8398386/SRX8398386.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 19:00:26: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:00:26: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:00:32: 1000000 INFO @ Sat, 15 Jan 2022 19:00:39: 2000000 INFO @ Sat, 15 Jan 2022 19:00:44: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 19:00:44: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 19:00:44: #1 total tags in treatment: 1359871 INFO @ Sat, 15 Jan 2022 19:00:44: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:00:44: #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 19:00:44: #1 tags after filtering in treatment: 1067869 INFO @ Sat, 15 Jan 2022 19:00:44: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Jan 2022 19:00:44: #1 finished! INFO @ Sat, 15 Jan 2022 19:00:44: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:00:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:00:44: #2 number of paired peaks: 135 WARNING @ Sat, 15 Jan 2022 19:00:44: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Sat, 15 Jan 2022 19:00:44: start model_add_line... INFO @ Sat, 15 Jan 2022 19:00:44: start X-correlation... INFO @ Sat, 15 Jan 2022 19:00:44: end of X-cor INFO @ Sat, 15 Jan 2022 19:00:44: #2 finished! INFO @ Sat, 15 Jan 2022 19:00:44: #2 predicted fragment length is 106 bps INFO @ Sat, 15 Jan 2022 19:00:44: #2 alternative fragment length(s) may be 9,60,74,106,153,186,248,382 bps INFO @ Sat, 15 Jan 2022 19:00:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8398386/SRX8398386.10_model.r INFO @ Sat, 15 Jan 2022 19:00:44: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:00:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:00:47: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:00:48: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8398386/SRX8398386.10_peaks.xls INFO @ Sat, 15 Jan 2022 19:00:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8398386/SRX8398386.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:00:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8398386/SRX8398386.10_summits.bed INFO @ Sat, 15 Jan 2022 19:00:48: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (38 records, 4 fields): 13 millis CompletedMACS2peakCalling 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 19:00:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8398386/SRX8398386.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8398386/SRX8398386.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8398386/SRX8398386.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8398386/SRX8398386.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 19:00:56: #1 read tag files... INFO @ Sat, 15 Jan 2022 19:00:56: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 19:01:03: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 19:01:11: 2000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 19:01:17: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 19:01:17: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 19:01:17: #1 total tags in treatment: 1359871 INFO @ Sat, 15 Jan 2022 19:01:17: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 19:01:17: #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 19:01:17: #1 tags after filtering in treatment: 1067869 INFO @ Sat, 15 Jan 2022 19:01:17: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Jan 2022 19:01:17: #1 finished! INFO @ Sat, 15 Jan 2022 19:01:17: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 19:01:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 19:01:17: #2 number of paired peaks: 135 WARNING @ Sat, 15 Jan 2022 19:01:17: Fewer paired peaks (135) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 135 pairs to build model! INFO @ Sat, 15 Jan 2022 19:01:17: start model_add_line... INFO @ Sat, 15 Jan 2022 19:01:17: start X-correlation... INFO @ Sat, 15 Jan 2022 19:01:17: end of X-cor INFO @ Sat, 15 Jan 2022 19:01:17: #2 finished! INFO @ Sat, 15 Jan 2022 19:01:17: #2 predicted fragment length is 106 bps INFO @ Sat, 15 Jan 2022 19:01:17: #2 alternative fragment length(s) may be 9,60,74,106,153,186,248,382 bps INFO @ Sat, 15 Jan 2022 19:01:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8398386/SRX8398386.20_model.r INFO @ Sat, 15 Jan 2022 19:01:17: #3 Call peaks... INFO @ Sat, 15 Jan 2022 19:01:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 19:01:20: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 19:01:21: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8398386/SRX8398386.20_peaks.xls INFO @ Sat, 15 Jan 2022 19:01:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8398386/SRX8398386.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 19:01:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8398386/SRX8398386.20_summits.bed INFO @ Sat, 15 Jan 2022 19:01:21: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (5 records, 4 fields): 25 millis CompletedMACS2peakCalling