Job ID = 6368451 SRX = SRX4996807 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-16T00:18:21 prefetch.2.10.7: 1) Downloading 'SRR8176693'... 2020-06-16T00:18:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:22:48 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:22:48 prefetch.2.10.7: 1) 'SRR8176693' was downloaded successfully 2020-06-16T00:22:48 prefetch.2.10.7: 'SRR8176693' has 0 unresolved dependencies Read 20945035 spots for SRR8176693/SRR8176693.sra Written 20945035 spots for SRR8176693/SRR8176693.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: 00:06:55 20945035 reads; of these: 20945035 (100.00%) were paired; of these: 16484170 (78.70%) aligned concordantly 0 times 3745029 (17.88%) aligned concordantly exactly 1 time 715836 (3.42%) aligned concordantly >1 times ---- 16484170 pairs aligned concordantly 0 times; of these: 55685 (0.34%) aligned discordantly 1 time ---- 16428485 pairs aligned 0 times concordantly or discordantly; of these: 32856970 mates make up the pairs; of these: 32771216 (99.74%) aligned 0 times 55019 (0.17%) aligned exactly 1 time 30735 (0.09%) aligned >1 times 21.77% overall alignment rate Time searching: 00:06:55 Overall time: 00:06:55 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 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 chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 542228 / 4514688 = 0.1201 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 @ Tue, 16 Jun 2020 09:34:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4996807/SRX4996807.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4996807/SRX4996807.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4996807/SRX4996807.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4996807/SRX4996807.bam'] # control file = None # effective genome size = 9.00e+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 @ Tue, 16 Jun 2020 09:34:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:35:04: 1000000 INFO @ Tue, 16 Jun 2020 09:35:09: 2000000 INFO @ Tue, 16 Jun 2020 09:35:13: 3000000 INFO @ Tue, 16 Jun 2020 09:35:18: 4000000 INFO @ Tue, 16 Jun 2020 09:35:22: 5000000 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 @ Tue, 16 Jun 2020 09:35:27: 6000000 INFO @ Tue, 16 Jun 2020 09:35:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4996807/SRX4996807.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4996807/SRX4996807.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4996807/SRX4996807.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4996807/SRX4996807.bam'] # control file = None # effective genome size = 9.00e+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 @ Tue, 16 Jun 2020 09:35:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:35:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:35:32: 7000000 INFO @ Tue, 16 Jun 2020 09:35:34: 1000000 INFO @ Tue, 16 Jun 2020 09:35:37: 8000000 INFO @ Tue, 16 Jun 2020 09:35:37: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:35:37: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:35:37: #1 total tags in treatment: 3920932 INFO @ Tue, 16 Jun 2020 09:35:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:35:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:35:37: #1 tags after filtering in treatment: 3776233 INFO @ Tue, 16 Jun 2020 09:35:37: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 16 Jun 2020 09:35:37: #1 finished! INFO @ Tue, 16 Jun 2020 09:35:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:35:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:35:37: #2 number of paired peaks: 483 WARNING @ Tue, 16 Jun 2020 09:35:37: Fewer paired peaks (483) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 483 pairs to build model! INFO @ Tue, 16 Jun 2020 09:35:37: start model_add_line... INFO @ Tue, 16 Jun 2020 09:35:37: start X-correlation... INFO @ Tue, 16 Jun 2020 09:35:37: end of X-cor INFO @ Tue, 16 Jun 2020 09:35:37: #2 finished! INFO @ Tue, 16 Jun 2020 09:35:37: #2 predicted fragment length is 160 bps INFO @ Tue, 16 Jun 2020 09:35:37: #2 alternative fragment length(s) may be 160,182 bps INFO @ Tue, 16 Jun 2020 09:35:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4996807/SRX4996807.05_model.r INFO @ Tue, 16 Jun 2020 09:35:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:35:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:35:39: 2000000 INFO @ Tue, 16 Jun 2020 09:35:44: 3000000 INFO @ Tue, 16 Jun 2020 09:35:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:35:48: 4000000 INFO @ Tue, 16 Jun 2020 09:35:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4996807/SRX4996807.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:35:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4996807/SRX4996807.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:35:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4996807/SRX4996807.05_summits.bed INFO @ Tue, 16 Jun 2020 09:35:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (288 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:35:53: 5000000 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 @ Tue, 16 Jun 2020 09:35:57: 6000000 INFO @ Tue, 16 Jun 2020 09:35:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4996807/SRX4996807.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4996807/SRX4996807.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4996807/SRX4996807.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4996807/SRX4996807.bam'] # control file = None # effective genome size = 9.00e+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 @ Tue, 16 Jun 2020 09:35:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:35:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:36:02: 7000000 INFO @ Tue, 16 Jun 2020 09:36:04: 1000000 INFO @ Tue, 16 Jun 2020 09:36:06: 8000000 INFO @ Tue, 16 Jun 2020 09:36:07: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:36:07: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:36:07: #1 total tags in treatment: 3920932 INFO @ Tue, 16 Jun 2020 09:36:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:36:07: #1 tags after filtering in treatment: 3776233 INFO @ Tue, 16 Jun 2020 09:36:07: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 16 Jun 2020 09:36:07: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:07: #2 number of paired peaks: 483 WARNING @ Tue, 16 Jun 2020 09:36:07: Fewer paired peaks (483) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 483 pairs to build model! INFO @ Tue, 16 Jun 2020 09:36:07: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:07: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:07: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:07: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:07: #2 predicted fragment length is 160 bps INFO @ Tue, 16 Jun 2020 09:36:07: #2 alternative fragment length(s) may be 160,182 bps INFO @ Tue, 16 Jun 2020 09:36:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4996807/SRX4996807.10_model.r INFO @ Tue, 16 Jun 2020 09:36:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:36:09: 2000000 INFO @ Tue, 16 Jun 2020 09:36:14: 3000000 INFO @ Tue, 16 Jun 2020 09:36:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:36:19: 4000000 INFO @ Tue, 16 Jun 2020 09:36:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4996807/SRX4996807.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4996807/SRX4996807.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4996807/SRX4996807.10_summits.bed INFO @ Tue, 16 Jun 2020 09:36:19: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (205 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:36:23: 5000000 INFO @ Tue, 16 Jun 2020 09:36:28: 6000000 INFO @ Tue, 16 Jun 2020 09:36:33: 7000000 INFO @ Tue, 16 Jun 2020 09:36:37: 8000000 INFO @ Tue, 16 Jun 2020 09:36:37: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:36:37: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:36:37: #1 total tags in treatment: 3920932 INFO @ Tue, 16 Jun 2020 09:36:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:36:38: #1 tags after filtering in treatment: 3776233 INFO @ Tue, 16 Jun 2020 09:36:38: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 16 Jun 2020 09:36:38: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:38: #2 number of paired peaks: 483 WARNING @ Tue, 16 Jun 2020 09:36:38: Fewer paired peaks (483) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 483 pairs to build model! INFO @ Tue, 16 Jun 2020 09:36:38: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:38: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:38: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:38: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:38: #2 predicted fragment length is 160 bps INFO @ Tue, 16 Jun 2020 09:36:38: #2 alternative fragment length(s) may be 160,182 bps INFO @ Tue, 16 Jun 2020 09:36:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4996807/SRX4996807.20_model.r INFO @ Tue, 16 Jun 2020 09:36:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:38: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:36:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:36:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4996807/SRX4996807.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4996807/SRX4996807.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4996807/SRX4996807.20_summits.bed INFO @ Tue, 16 Jun 2020 09:36:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (135 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。