Job ID = 14520194 SRX = SRX7496393 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2074371 spots for SRR10823004/SRR10823004.sra Written 2074371 spots for SRR10823004/SRR10823004.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: 00:01:13 2074371 reads; of these: 2074371 (100.00%) were paired; of these: 946410 (45.62%) aligned concordantly 0 times 1006389 (48.52%) aligned concordantly exactly 1 time 121572 (5.86%) aligned concordantly >1 times ---- 946410 pairs aligned concordantly 0 times; of these: 7390 (0.78%) aligned discordantly 1 time ---- 939020 pairs aligned 0 times concordantly or discordantly; of these: 1878040 mates make up the pairs; of these: 1013626 (53.97%) aligned 0 times 765855 (40.78%) aligned exactly 1 time 98559 (5.25%) aligned >1 times 75.57% overall alignment rate Time searching: 00:01:13 Overall time: 00:01:13 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] 34296 / 1134920 = 0.0302 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 18:36:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7496393/SRX7496393.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7496393/SRX7496393.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7496393/SRX7496393.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7496393/SRX7496393.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 18:36:39: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:36:39: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:36:44: 1000000 INFO @ Sat, 15 Jan 2022 18:36:49: 2000000 INFO @ Sat, 15 Jan 2022 18:36:53: 3000000 INFO @ Sat, 15 Jan 2022 18:36:54: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 18:36:54: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 18:36:54: #1 total tags in treatment: 1093722 INFO @ Sat, 15 Jan 2022 18:36:54: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:36:54: #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 18:36:54: #1 tags after filtering in treatment: 912100 INFO @ Sat, 15 Jan 2022 18:36:54: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 15 Jan 2022 18:36:54: #1 finished! INFO @ Sat, 15 Jan 2022 18:36:54: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:36:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:36:54: #2 number of paired peaks: 136 WARNING @ Sat, 15 Jan 2022 18:36:54: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Sat, 15 Jan 2022 18:36:54: start model_add_line... INFO @ Sat, 15 Jan 2022 18:36:54: start X-correlation... INFO @ Sat, 15 Jan 2022 18:36:54: end of X-cor INFO @ Sat, 15 Jan 2022 18:36:54: #2 finished! INFO @ Sat, 15 Jan 2022 18:36:54: #2 predicted fragment length is 258 bps INFO @ Sat, 15 Jan 2022 18:36:54: #2 alternative fragment length(s) may be 73,258,275,320,461,529,557,578,580 bps INFO @ Sat, 15 Jan 2022 18:36:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7496393/SRX7496393.05_model.r INFO @ Sat, 15 Jan 2022 18:36:54: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:36:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:36:56: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:36:57: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7496393/SRX7496393.05_peaks.xls INFO @ Sat, 15 Jan 2022 18:36:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7496393/SRX7496393.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:36:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7496393/SRX7496393.05_summits.bed INFO @ Sat, 15 Jan 2022 18:36:57: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (19 records, 4 fields): 1 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 18:37:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7496393/SRX7496393.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7496393/SRX7496393.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7496393/SRX7496393.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7496393/SRX7496393.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 18:37:09: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:37:09: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:37:14: 1000000 INFO @ Sat, 15 Jan 2022 18:37:18: 2000000 INFO @ Sat, 15 Jan 2022 18:37:23: 3000000 INFO @ Sat, 15 Jan 2022 18:37:23: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 18:37:23: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 18:37:23: #1 total tags in treatment: 1093722 INFO @ Sat, 15 Jan 2022 18:37:23: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:37:23: #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 18:37:23: #1 tags after filtering in treatment: 912100 INFO @ Sat, 15 Jan 2022 18:37:23: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 15 Jan 2022 18:37:23: #1 finished! INFO @ Sat, 15 Jan 2022 18:37:23: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:37:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:37:23: #2 number of paired peaks: 136 WARNING @ Sat, 15 Jan 2022 18:37:23: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Sat, 15 Jan 2022 18:37:23: start model_add_line... INFO @ Sat, 15 Jan 2022 18:37:23: start X-correlation... INFO @ Sat, 15 Jan 2022 18:37:23: end of X-cor INFO @ Sat, 15 Jan 2022 18:37:23: #2 finished! INFO @ Sat, 15 Jan 2022 18:37:23: #2 predicted fragment length is 258 bps INFO @ Sat, 15 Jan 2022 18:37:23: #2 alternative fragment length(s) may be 73,258,275,320,461,529,557,578,580 bps INFO @ Sat, 15 Jan 2022 18:37:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7496393/SRX7496393.10_model.r INFO @ Sat, 15 Jan 2022 18:37:24: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:37:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:37:27: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:37:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7496393/SRX7496393.10_peaks.xls INFO @ Sat, 15 Jan 2022 18:37:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7496393/SRX7496393.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:37:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7496393/SRX7496393.10_summits.bed INFO @ Sat, 15 Jan 2022 18:37:28: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (5 records, 4 fields): 3 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 18:37:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7496393/SRX7496393.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7496393/SRX7496393.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7496393/SRX7496393.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7496393/SRX7496393.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 18:37:39: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:37:39: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:37:44: 1000000 INFO @ Sat, 15 Jan 2022 18:37:50: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 18:37:55: 3000000 INFO @ Sat, 15 Jan 2022 18:37:56: #1 tag size is determined as 37 bps INFO @ Sat, 15 Jan 2022 18:37:56: #1 tag size = 37 INFO @ Sat, 15 Jan 2022 18:37:56: #1 total tags in treatment: 1093722 INFO @ Sat, 15 Jan 2022 18:37:56: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:37:56: #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 18:37:56: #1 tags after filtering in treatment: 912100 INFO @ Sat, 15 Jan 2022 18:37:56: #1 Redundant rate of treatment: 0.17 INFO @ Sat, 15 Jan 2022 18:37:56: #1 finished! INFO @ Sat, 15 Jan 2022 18:37:56: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:37:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:37:56: #2 number of paired peaks: 136 WARNING @ Sat, 15 Jan 2022 18:37:56: Fewer paired peaks (136) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 136 pairs to build model! INFO @ Sat, 15 Jan 2022 18:37:56: start model_add_line... INFO @ Sat, 15 Jan 2022 18:37:56: start X-correlation... INFO @ Sat, 15 Jan 2022 18:37:56: end of X-cor INFO @ Sat, 15 Jan 2022 18:37:56: #2 finished! INFO @ Sat, 15 Jan 2022 18:37:56: #2 predicted fragment length is 258 bps INFO @ Sat, 15 Jan 2022 18:37:56: #2 alternative fragment length(s) may be 73,258,275,320,461,529,557,578,580 bps INFO @ Sat, 15 Jan 2022 18:37:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7496393/SRX7496393.20_model.r INFO @ Sat, 15 Jan 2022 18:37:56: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:37:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:37:58: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 18:37:59: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7496393/SRX7496393.20_peaks.xls INFO @ Sat, 15 Jan 2022 18:37:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7496393/SRX7496393.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:37:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7496393/SRX7496393.20_summits.bed INFO @ Sat, 15 Jan 2022 18:37:59: Done! pass1 - making usageList (1 chroms): 0 millis pass2 - checking and writing primary data (2 records, 4 fields): 1 millis CompletedMACS2peakCalling