Job ID = 7107284 SRX = SRX6911549 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 1507530 spots for SRR10191176/SRR10191176.sra Written 1507530 spots for SRR10191176/SRR10191176.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: 00:01:06 1507530 reads; of these: 1507530 (100.00%) were paired; of these: 784728 (52.05%) aligned concordantly 0 times 546538 (36.25%) aligned concordantly exactly 1 time 176264 (11.69%) aligned concordantly >1 times ---- 784728 pairs aligned concordantly 0 times; of these: 39987 (5.10%) aligned discordantly 1 time ---- 744741 pairs aligned 0 times concordantly or discordantly; of these: 1489482 mates make up the pairs; of these: 1418027 (95.20%) aligned 0 times 25149 (1.69%) aligned exactly 1 time 46306 (3.11%) aligned >1 times 52.97% overall alignment rate Time searching: 00:01:06 Overall time: 00:01:06 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] 177630 / 762682 = 0.2329 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 13:04:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911549/SRX6911549.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911549/SRX6911549.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911549/SRX6911549.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911549/SRX6911549.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 @ Wed, 22 Jul 2020 13:04:49: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:04:49: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:04:56: 1000000 INFO @ Wed, 22 Jul 2020 13:04:57: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 13:04:57: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 13:04:57: #1 total tags in treatment: 551967 INFO @ Wed, 22 Jul 2020 13:04:57: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:04:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 13:04:57: #1 tags after filtering in treatment: 444769 INFO @ Wed, 22 Jul 2020 13:04:57: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 22 Jul 2020 13:04:57: #1 finished! INFO @ Wed, 22 Jul 2020 13:04:57: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:04:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:04:58: #2 number of paired peaks: 185 WARNING @ Wed, 22 Jul 2020 13:04:58: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Wed, 22 Jul 2020 13:04:58: start model_add_line... INFO @ Wed, 22 Jul 2020 13:04:58: start X-correlation... INFO @ Wed, 22 Jul 2020 13:04:58: end of X-cor INFO @ Wed, 22 Jul 2020 13:04:58: #2 finished! INFO @ Wed, 22 Jul 2020 13:04:58: #2 predicted fragment length is 206 bps INFO @ Wed, 22 Jul 2020 13:04:58: #2 alternative fragment length(s) may be 4,153,175,190,206 bps INFO @ Wed, 22 Jul 2020 13:04:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911549/SRX6911549.05_model.r INFO @ Wed, 22 Jul 2020 13:04:58: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:04:58: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:04:59: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:04:59: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911549/SRX6911549.05_peaks.xls INFO @ Wed, 22 Jul 2020 13:04:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911549/SRX6911549.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:04:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911549/SRX6911549.05_summits.bed INFO @ Wed, 22 Jul 2020 13:04:59: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (117 records, 4 fields): 2 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 13:05:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911549/SRX6911549.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911549/SRX6911549.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911549/SRX6911549.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911549/SRX6911549.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 @ Wed, 22 Jul 2020 13:05:19: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:05:19: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 13:05:25: 1000000 INFO @ Wed, 22 Jul 2020 13:05:26: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 13:05:26: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 13:05:26: #1 total tags in treatment: 551967 INFO @ Wed, 22 Jul 2020 13:05:26: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:05:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 13:05:26: #1 tags after filtering in treatment: 444769 INFO @ Wed, 22 Jul 2020 13:05:26: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 22 Jul 2020 13:05:26: #1 finished! INFO @ Wed, 22 Jul 2020 13:05:26: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:05:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:05:26: #2 number of paired peaks: 185 WARNING @ Wed, 22 Jul 2020 13:05:26: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Wed, 22 Jul 2020 13:05:26: start model_add_line... INFO @ Wed, 22 Jul 2020 13:05:26: start X-correlation... INFO @ Wed, 22 Jul 2020 13:05:26: end of X-cor INFO @ Wed, 22 Jul 2020 13:05:26: #2 finished! INFO @ Wed, 22 Jul 2020 13:05:26: #2 predicted fragment length is 206 bps INFO @ Wed, 22 Jul 2020 13:05:26: #2 alternative fragment length(s) may be 4,153,175,190,206 bps INFO @ Wed, 22 Jul 2020 13:05:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911549/SRX6911549.10_model.r INFO @ Wed, 22 Jul 2020 13:05:26: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:05:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:05:28: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:05:28: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911549/SRX6911549.10_peaks.xls INFO @ Wed, 22 Jul 2020 13:05:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911549/SRX6911549.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:05:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911549/SRX6911549.10_summits.bed INFO @ Wed, 22 Jul 2020 13:05:28: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (46 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 13:05:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX6911549/SRX6911549.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX6911549/SRX6911549.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX6911549/SRX6911549.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX6911549/SRX6911549.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 @ Wed, 22 Jul 2020 13:05:49: #1 read tag files... INFO @ Wed, 22 Jul 2020 13:05:49: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 13:05:56: 1000000 INFO @ Wed, 22 Jul 2020 13:05:57: #1 tag size is determined as 101 bps INFO @ Wed, 22 Jul 2020 13:05:57: #1 tag size = 101 INFO @ Wed, 22 Jul 2020 13:05:57: #1 total tags in treatment: 551967 INFO @ Wed, 22 Jul 2020 13:05:57: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 13:05:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 13:05:57: #1 tags after filtering in treatment: 444769 INFO @ Wed, 22 Jul 2020 13:05:57: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 22 Jul 2020 13:05:57: #1 finished! INFO @ Wed, 22 Jul 2020 13:05:57: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 13:05:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 13:05:57: #2 number of paired peaks: 185 WARNING @ Wed, 22 Jul 2020 13:05:57: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Wed, 22 Jul 2020 13:05:57: start model_add_line... INFO @ Wed, 22 Jul 2020 13:05:57: start X-correlation... INFO @ Wed, 22 Jul 2020 13:05:57: end of X-cor INFO @ Wed, 22 Jul 2020 13:05:57: #2 finished! INFO @ Wed, 22 Jul 2020 13:05:57: #2 predicted fragment length is 206 bps INFO @ Wed, 22 Jul 2020 13:05:57: #2 alternative fragment length(s) may be 4,153,175,190,206 bps INFO @ Wed, 22 Jul 2020 13:05:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX6911549/SRX6911549.20_model.r INFO @ Wed, 22 Jul 2020 13:05:57: #3 Call peaks... INFO @ Wed, 22 Jul 2020 13:05:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 13:05:58: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 13:05:59: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX6911549/SRX6911549.20_peaks.xls INFO @ Wed, 22 Jul 2020 13:05:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX6911549/SRX6911549.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 13:05:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX6911549/SRX6911549.20_summits.bed INFO @ Wed, 22 Jul 2020 13:05:59: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (17 records, 4 fields): 1 millis CompletedMACS2peakCalling