Job ID = 14519712 SRX = SRX8586261 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7718988 spots for SRR12057930/SRR12057930.sra Written 7718988 spots for SRR12057930/SRR12057930.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: 00:05:01 7718988 reads; of these: 7718988 (100.00%) were paired; of these: 1146456 (14.85%) aligned concordantly 0 times 4062677 (52.63%) aligned concordantly exactly 1 time 2509855 (32.52%) aligned concordantly >1 times ---- 1146456 pairs aligned concordantly 0 times; of these: 33040 (2.88%) aligned discordantly 1 time ---- 1113416 pairs aligned 0 times concordantly or discordantly; of these: 2226832 mates make up the pairs; of these: 2106837 (94.61%) aligned 0 times 59395 (2.67%) aligned exactly 1 time 60600 (2.72%) aligned >1 times 86.35% overall alignment rate Time searching: 00:05:01 Overall time: 00:05:01 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] 2782813 / 6605124 = 0.4213 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 17:39:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8586261/SRX8586261.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8586261/SRX8586261.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8586261/SRX8586261.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8586261/SRX8586261.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 17:39:39: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:39:39: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:39:45: 1000000 INFO @ Sat, 15 Jan 2022 17:39:51: 2000000 INFO @ Sat, 15 Jan 2022 17:39:58: 3000000 INFO @ Sat, 15 Jan 2022 17:40:04: 4000000 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 17:40:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8586261/SRX8586261.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8586261/SRX8586261.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8586261/SRX8586261.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8586261/SRX8586261.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 17:40:09: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:40:09: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:40:11: 5000000 INFO @ Sat, 15 Jan 2022 17:40:15: 1000000 INFO @ Sat, 15 Jan 2022 17:40:17: 6000000 INFO @ Sat, 15 Jan 2022 17:40:21: 2000000 INFO @ Sat, 15 Jan 2022 17:40:24: 7000000 INFO @ Sat, 15 Jan 2022 17:40:28: 3000000 INFO @ Sat, 15 Jan 2022 17:40:29: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 17:40:29: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 17:40:29: #1 total tags in treatment: 3796506 INFO @ Sat, 15 Jan 2022 17:40:29: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:40:29: #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 17:40:29: #1 tags after filtering in treatment: 2098507 INFO @ Sat, 15 Jan 2022 17:40:29: #1 Redundant rate of treatment: 0.45 INFO @ Sat, 15 Jan 2022 17:40:29: #1 finished! INFO @ Sat, 15 Jan 2022 17:40:29: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:40:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:40:29: #2 number of paired peaks: 175 WARNING @ Sat, 15 Jan 2022 17:40:29: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Sat, 15 Jan 2022 17:40:29: start model_add_line... INFO @ Sat, 15 Jan 2022 17:40:29: start X-correlation... INFO @ Sat, 15 Jan 2022 17:40:29: end of X-cor INFO @ Sat, 15 Jan 2022 17:40:29: #2 finished! INFO @ Sat, 15 Jan 2022 17:40:29: #2 predicted fragment length is 147 bps INFO @ Sat, 15 Jan 2022 17:40:29: #2 alternative fragment length(s) may be 0,147,176,537,579 bps INFO @ Sat, 15 Jan 2022 17:40:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8586261/SRX8586261.05_model.r INFO @ Sat, 15 Jan 2022 17:40:29: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:40:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:40:34: 4000000 INFO @ Sat, 15 Jan 2022 17:40:35: #3 Call peaks for each chromosome... 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 17:40:38: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8586261/SRX8586261.05_peaks.xls INFO @ Sat, 15 Jan 2022 17:40:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8586261/SRX8586261.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:40:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8586261/SRX8586261.05_summits.bed INFO @ Sat, 15 Jan 2022 17:40:38: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (32 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:40:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8586261/SRX8586261.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8586261/SRX8586261.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8586261/SRX8586261.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8586261/SRX8586261.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 17:40:38: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:40:38: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:40:40: 5000000 INFO @ Sat, 15 Jan 2022 17:40:46: 6000000 INFO @ Sat, 15 Jan 2022 17:40:46: 1000000 INFO @ Sat, 15 Jan 2022 17:40:52: 7000000 INFO @ Sat, 15 Jan 2022 17:40:53: 2000000 INFO @ Sat, 15 Jan 2022 17:40:56: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 17:40:56: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 17:40:56: #1 total tags in treatment: 3796506 INFO @ Sat, 15 Jan 2022 17:40:56: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:40:56: #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 17:40:56: #1 tags after filtering in treatment: 2098507 INFO @ Sat, 15 Jan 2022 17:40:56: #1 Redundant rate of treatment: 0.45 INFO @ Sat, 15 Jan 2022 17:40:56: #1 finished! INFO @ Sat, 15 Jan 2022 17:40:56: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:40:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:40:57: #2 number of paired peaks: 175 WARNING @ Sat, 15 Jan 2022 17:40:57: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Sat, 15 Jan 2022 17:40:57: start model_add_line... INFO @ Sat, 15 Jan 2022 17:40:57: start X-correlation... INFO @ Sat, 15 Jan 2022 17:40:57: end of X-cor INFO @ Sat, 15 Jan 2022 17:40:57: #2 finished! INFO @ Sat, 15 Jan 2022 17:40:57: #2 predicted fragment length is 147 bps INFO @ Sat, 15 Jan 2022 17:40:57: #2 alternative fragment length(s) may be 0,147,176,537,579 bps INFO @ Sat, 15 Jan 2022 17:40:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8586261/SRX8586261.10_model.r INFO @ Sat, 15 Jan 2022 17:40:57: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:40:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:41:00: 3000000 INFO @ Sat, 15 Jan 2022 17:41:03: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:41:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8586261/SRX8586261.10_peaks.xls INFO @ Sat, 15 Jan 2022 17:41:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8586261/SRX8586261.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:41:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8586261/SRX8586261.10_summits.bed INFO @ Sat, 15 Jan 2022 17:41:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (16 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:41:07: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 17:41:14: 5000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 17:41:20: 6000000 INFO @ Sat, 15 Jan 2022 17:41:27: 7000000 INFO @ Sat, 15 Jan 2022 17:41:32: #1 tag size is determined as 40 bps INFO @ Sat, 15 Jan 2022 17:41:32: #1 tag size = 40 INFO @ Sat, 15 Jan 2022 17:41:32: #1 total tags in treatment: 3796506 INFO @ Sat, 15 Jan 2022 17:41:32: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:41:32: #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 17:41:32: #1 tags after filtering in treatment: 2098507 INFO @ Sat, 15 Jan 2022 17:41:32: #1 Redundant rate of treatment: 0.45 INFO @ Sat, 15 Jan 2022 17:41:32: #1 finished! INFO @ Sat, 15 Jan 2022 17:41:32: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:41:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:41:32: #2 number of paired peaks: 175 WARNING @ Sat, 15 Jan 2022 17:41:32: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Sat, 15 Jan 2022 17:41:32: start model_add_line... INFO @ Sat, 15 Jan 2022 17:41:32: start X-correlation... INFO @ Sat, 15 Jan 2022 17:41:32: end of X-cor INFO @ Sat, 15 Jan 2022 17:41:32: #2 finished! INFO @ Sat, 15 Jan 2022 17:41:32: #2 predicted fragment length is 147 bps INFO @ Sat, 15 Jan 2022 17:41:32: #2 alternative fragment length(s) may be 0,147,176,537,579 bps INFO @ Sat, 15 Jan 2022 17:41:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8586261/SRX8586261.20_model.r INFO @ Sat, 15 Jan 2022 17:41:32: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:41:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:41:38: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:41:41: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8586261/SRX8586261.20_peaks.xls INFO @ Sat, 15 Jan 2022 17:41:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8586261/SRX8586261.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:41:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8586261/SRX8586261.20_summits.bed INFO @ Sat, 15 Jan 2022 17:41:41: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (2 records, 4 fields): 2 millis CompletedMACS2peakCalling