Job ID = 6367869 SRX = SRX4085436 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:42:59 prefetch.2.10.7: 1) Downloading 'SRR7167465'... 2020-06-15T23:42:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:51:13 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:51:13 prefetch.2.10.7: 1) 'SRR7167465' was downloaded successfully Read 24333421 spots for SRR7167465/SRR7167465.sra Written 24333421 spots for SRR7167465/SRR7167465.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: 00:11:10 24333421 reads; of these: 24333421 (100.00%) were paired; of these: 16443007 (67.57%) aligned concordantly 0 times 6714622 (27.59%) aligned concordantly exactly 1 time 1175792 (4.83%) aligned concordantly >1 times ---- 16443007 pairs aligned concordantly 0 times; of these: 102628 (0.62%) aligned discordantly 1 time ---- 16340379 pairs aligned 0 times concordantly or discordantly; of these: 32680758 mates make up the pairs; of these: 29131383 (89.14%) aligned 0 times 3095459 (9.47%) aligned exactly 1 time 453916 (1.39%) aligned >1 times 40.14% overall alignment rate Time searching: 00:11:11 Overall time: 00:11:11 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_sort_core] merging from 8 files... [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] 3291100 / 7958515 = 0.4135 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 09:10:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085436/SRX4085436.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085436/SRX4085436.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085436/SRX4085436.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085436/SRX4085436.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 09:10:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:39: 1000000 INFO @ Tue, 16 Jun 2020 09:10:46: 2000000 INFO @ Tue, 16 Jun 2020 09:10:53: 3000000 INFO @ Tue, 16 Jun 2020 09:10:59: 4000000 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 09:11:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085436/SRX4085436.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085436/SRX4085436.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085436/SRX4085436.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085436/SRX4085436.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 09:11:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:07: 5000000 INFO @ Tue, 16 Jun 2020 09:11:10: 1000000 INFO @ Tue, 16 Jun 2020 09:11:15: 6000000 INFO @ Tue, 16 Jun 2020 09:11:17: 2000000 INFO @ Tue, 16 Jun 2020 09:11:23: 7000000 INFO @ Tue, 16 Jun 2020 09:11:25: 3000000 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 09:11:30: 8000000 INFO @ Tue, 16 Jun 2020 09:11:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085436/SRX4085436.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085436/SRX4085436.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085436/SRX4085436.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085436/SRX4085436.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 09:11:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:32: 4000000 INFO @ Tue, 16 Jun 2020 09:11:38: 9000000 INFO @ Tue, 16 Jun 2020 09:11:40: 1000000 INFO @ Tue, 16 Jun 2020 09:11:40: 5000000 INFO @ Tue, 16 Jun 2020 09:11:46: 10000000 INFO @ Tue, 16 Jun 2020 09:11:47: 2000000 INFO @ Tue, 16 Jun 2020 09:11:47: 6000000 INFO @ Tue, 16 Jun 2020 09:11:54: 11000000 INFO @ Tue, 16 Jun 2020 09:11:55: 3000000 INFO @ Tue, 16 Jun 2020 09:11:55: 7000000 INFO @ Tue, 16 Jun 2020 09:12:01: 12000000 INFO @ Tue, 16 Jun 2020 09:12:02: 4000000 INFO @ Tue, 16 Jun 2020 09:12:02: 8000000 INFO @ Tue, 16 Jun 2020 09:12:08: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:12:08: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:12:08: #1 total tags in treatment: 4621959 INFO @ Tue, 16 Jun 2020 09:12:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:08: #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 09:12:08: #1 tags after filtering in treatment: 4238730 INFO @ Tue, 16 Jun 2020 09:12:08: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 16 Jun 2020 09:12:08: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:08: #2 number of paired peaks: 430 WARNING @ Tue, 16 Jun 2020 09:12:08: Fewer paired peaks (430) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 430 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:08: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:08: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:08: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:08: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:08: #2 predicted fragment length is 131 bps INFO @ Tue, 16 Jun 2020 09:12:08: #2 alternative fragment length(s) may be 131 bps INFO @ Tue, 16 Jun 2020 09:12:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085436/SRX4085436.05_model.r INFO @ Tue, 16 Jun 2020 09:12:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:09: 5000000 INFO @ Tue, 16 Jun 2020 09:12:10: 9000000 INFO @ Tue, 16 Jun 2020 09:12:16: 10000000 INFO @ Tue, 16 Jun 2020 09:12:16: 6000000 INFO @ Tue, 16 Jun 2020 09:12:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:23: 11000000 INFO @ Tue, 16 Jun 2020 09:12:23: 7000000 INFO @ Tue, 16 Jun 2020 09:12:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085436/SRX4085436.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085436/SRX4085436.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085436/SRX4085436.05_summits.bed INFO @ Tue, 16 Jun 2020 09:12:23: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (547 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:12:30: 12000000 INFO @ Tue, 16 Jun 2020 09:12:30: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:12:35: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:12:35: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:12:35: #1 total tags in treatment: 4621959 INFO @ Tue, 16 Jun 2020 09:12:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:35: #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 09:12:36: #1 tags after filtering in treatment: 4238730 INFO @ Tue, 16 Jun 2020 09:12:36: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 16 Jun 2020 09:12:36: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:36: #2 number of paired peaks: 430 WARNING @ Tue, 16 Jun 2020 09:12:36: Fewer paired peaks (430) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 430 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:36: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:36: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:36: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:36: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:36: #2 predicted fragment length is 131 bps INFO @ Tue, 16 Jun 2020 09:12:36: #2 alternative fragment length(s) may be 131 bps INFO @ Tue, 16 Jun 2020 09:12:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085436/SRX4085436.10_model.r INFO @ Tue, 16 Jun 2020 09:12:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:36: 9000000 INFO @ Tue, 16 Jun 2020 09:12:42: 10000000 INFO @ Tue, 16 Jun 2020 09:12:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:48: 11000000 INFO @ Tue, 16 Jun 2020 09:12:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085436/SRX4085436.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085436/SRX4085436.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085436/SRX4085436.10_summits.bed INFO @ Tue, 16 Jun 2020 09:12:51: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (310 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:12:54: 12000000 INFO @ Tue, 16 Jun 2020 09:12:59: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:12:59: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:12:59: #1 total tags in treatment: 4621959 INFO @ Tue, 16 Jun 2020 09:12:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:59: #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 09:12:59: #1 tags after filtering in treatment: 4238730 INFO @ Tue, 16 Jun 2020 09:12:59: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 16 Jun 2020 09:12:59: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:59: #2 number of paired peaks: 430 WARNING @ Tue, 16 Jun 2020 09:12:59: Fewer paired peaks (430) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 430 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:59: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:59: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:59: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:59: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:59: #2 predicted fragment length is 131 bps INFO @ Tue, 16 Jun 2020 09:12:59: #2 alternative fragment length(s) may be 131 bps INFO @ Tue, 16 Jun 2020 09:12:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085436/SRX4085436.20_model.r INFO @ Tue, 16 Jun 2020 09:12:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:59: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:13:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:13:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085436/SRX4085436.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085436/SRX4085436.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085436/SRX4085436.20_summits.bed INFO @ Tue, 16 Jun 2020 09:13:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (151 records, 4 fields): 1 millis CompletedMACS2peakCalling