Job ID = 6368452 SRX = SRX4996808 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-16T00:12:35 prefetch.2.10.7: 1) Downloading 'SRR8176694'... 2020-06-16T00:12:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:15:23 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:15:23 prefetch.2.10.7: 1) 'SRR8176694' was downloaded successfully 2020-06-16T00:15:23 prefetch.2.10.7: 'SRR8176694' has 0 unresolved dependencies Read 16457303 spots for SRR8176694/SRR8176694.sra Written 16457303 spots for SRR8176694/SRR8176694.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: 00:14:17 16457303 reads; of these: 16457303 (100.00%) were paired; of these: 3086150 (18.75%) aligned concordantly 0 times 11174165 (67.90%) aligned concordantly exactly 1 time 2196988 (13.35%) aligned concordantly >1 times ---- 3086150 pairs aligned concordantly 0 times; of these: 1140976 (36.97%) aligned discordantly 1 time ---- 1945174 pairs aligned 0 times concordantly or discordantly; of these: 3890348 mates make up the pairs; of these: 3289406 (84.55%) aligned 0 times 293145 (7.54%) aligned exactly 1 time 307797 (7.91%) aligned >1 times 90.01% overall alignment rate Time searching: 00:14:17 Overall time: 00:14:17 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 16 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] 4147787 / 14502944 = 0.2860 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 09:37:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4996808/SRX4996808.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4996808/SRX4996808.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4996808/SRX4996808.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4996808/SRX4996808.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 09:37:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:37:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:37:33: 1000000 INFO @ Tue, 16 Jun 2020 09:37:38: 2000000 INFO @ Tue, 16 Jun 2020 09:37:42: 3000000 INFO @ Tue, 16 Jun 2020 09:37:46: 4000000 INFO @ Tue, 16 Jun 2020 09:37:51: 5000000 INFO @ Tue, 16 Jun 2020 09:37:55: 6000000 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 09:37:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4996808/SRX4996808.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4996808/SRX4996808.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4996808/SRX4996808.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4996808/SRX4996808.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 09:37:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:37:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:38:00: 7000000 INFO @ Tue, 16 Jun 2020 09:38:04: 1000000 INFO @ Tue, 16 Jun 2020 09:38:05: 8000000 INFO @ Tue, 16 Jun 2020 09:38:09: 2000000 INFO @ Tue, 16 Jun 2020 09:38:10: 9000000 INFO @ Tue, 16 Jun 2020 09:38:14: 3000000 INFO @ Tue, 16 Jun 2020 09:38:15: 10000000 INFO @ Tue, 16 Jun 2020 09:38:19: 4000000 INFO @ Tue, 16 Jun 2020 09:38:19: 11000000 INFO @ Tue, 16 Jun 2020 09:38:24: 5000000 INFO @ Tue, 16 Jun 2020 09:38:24: 12000000 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 09:38:29: 6000000 INFO @ Tue, 16 Jun 2020 09:38:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4996808/SRX4996808.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4996808/SRX4996808.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4996808/SRX4996808.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4996808/SRX4996808.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 09:38:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:38:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:38:29: 13000000 INFO @ Tue, 16 Jun 2020 09:38:34: 7000000 INFO @ Tue, 16 Jun 2020 09:38:34: 14000000 INFO @ Tue, 16 Jun 2020 09:38:34: 1000000 INFO @ Tue, 16 Jun 2020 09:38:39: 8000000 INFO @ Tue, 16 Jun 2020 09:38:39: 15000000 INFO @ Tue, 16 Jun 2020 09:38:40: 2000000 INFO @ Tue, 16 Jun 2020 09:38:44: 9000000 INFO @ Tue, 16 Jun 2020 09:38:44: 16000000 INFO @ Tue, 16 Jun 2020 09:38:46: 3000000 INFO @ Tue, 16 Jun 2020 09:38:49: 10000000 INFO @ Tue, 16 Jun 2020 09:38:49: 17000000 INFO @ Tue, 16 Jun 2020 09:38:52: 4000000 INFO @ Tue, 16 Jun 2020 09:38:54: 11000000 INFO @ Tue, 16 Jun 2020 09:38:54: 18000000 INFO @ Tue, 16 Jun 2020 09:38:58: 5000000 INFO @ Tue, 16 Jun 2020 09:38:59: 12000000 INFO @ Tue, 16 Jun 2020 09:38:59: 19000000 INFO @ Tue, 16 Jun 2020 09:39:03: 6000000 INFO @ Tue, 16 Jun 2020 09:39:04: 13000000 INFO @ Tue, 16 Jun 2020 09:39:05: 20000000 INFO @ Tue, 16 Jun 2020 09:39:09: 14000000 INFO @ Tue, 16 Jun 2020 09:39:09: 7000000 INFO @ Tue, 16 Jun 2020 09:39:10: 21000000 INFO @ Tue, 16 Jun 2020 09:39:11: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:39:11: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:39:11: #1 total tags in treatment: 9382997 INFO @ Tue, 16 Jun 2020 09:39:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:39:11: #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 09:39:11: #1 tags after filtering in treatment: 8653003 INFO @ Tue, 16 Jun 2020 09:39:11: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 16 Jun 2020 09:39:11: #1 finished! INFO @ Tue, 16 Jun 2020 09:39:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:39:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:39:12: #2 number of paired peaks: 566 WARNING @ Tue, 16 Jun 2020 09:39:12: Fewer paired peaks (566) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 566 pairs to build model! INFO @ Tue, 16 Jun 2020 09:39:12: start model_add_line... INFO @ Tue, 16 Jun 2020 09:39:12: start X-correlation... INFO @ Tue, 16 Jun 2020 09:39:12: end of X-cor INFO @ Tue, 16 Jun 2020 09:39:12: #2 finished! INFO @ Tue, 16 Jun 2020 09:39:12: #2 predicted fragment length is 147 bps INFO @ Tue, 16 Jun 2020 09:39:12: #2 alternative fragment length(s) may be 4,147 bps INFO @ Tue, 16 Jun 2020 09:39:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4996808/SRX4996808.05_model.r INFO @ Tue, 16 Jun 2020 09:39:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:39:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:39:14: 15000000 INFO @ Tue, 16 Jun 2020 09:39:15: 8000000 INFO @ Tue, 16 Jun 2020 09:39:19: 16000000 INFO @ Tue, 16 Jun 2020 09:39:20: 9000000 INFO @ Tue, 16 Jun 2020 09:39:24: 17000000 INFO @ Tue, 16 Jun 2020 09:39:26: 10000000 INFO @ Tue, 16 Jun 2020 09:39:29: 18000000 INFO @ Tue, 16 Jun 2020 09:39:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:39:32: 11000000 INFO @ Tue, 16 Jun 2020 09:39:34: 19000000 INFO @ Tue, 16 Jun 2020 09:39:38: 12000000 INFO @ Tue, 16 Jun 2020 09:39:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4996808/SRX4996808.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:39:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4996808/SRX4996808.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:39:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4996808/SRX4996808.05_summits.bed INFO @ Tue, 16 Jun 2020 09:39:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (435 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:39:39: 20000000 INFO @ Tue, 16 Jun 2020 09:39:44: 13000000 INFO @ Tue, 16 Jun 2020 09:39:44: 21000000 INFO @ Tue, 16 Jun 2020 09:39:46: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:39:46: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:39:46: #1 total tags in treatment: 9382997 INFO @ Tue, 16 Jun 2020 09:39:46: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:39:46: #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 09:39:46: #1 tags after filtering in treatment: 8653003 INFO @ Tue, 16 Jun 2020 09:39:46: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 16 Jun 2020 09:39:46: #1 finished! INFO @ Tue, 16 Jun 2020 09:39:46: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:39:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:39:47: #2 number of paired peaks: 566 WARNING @ Tue, 16 Jun 2020 09:39:47: Fewer paired peaks (566) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 566 pairs to build model! INFO @ Tue, 16 Jun 2020 09:39:47: start model_add_line... INFO @ Tue, 16 Jun 2020 09:39:47: start X-correlation... INFO @ Tue, 16 Jun 2020 09:39:47: end of X-cor INFO @ Tue, 16 Jun 2020 09:39:47: #2 finished! INFO @ Tue, 16 Jun 2020 09:39:47: #2 predicted fragment length is 147 bps INFO @ Tue, 16 Jun 2020 09:39:47: #2 alternative fragment length(s) may be 4,147 bps INFO @ Tue, 16 Jun 2020 09:39:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4996808/SRX4996808.10_model.r INFO @ Tue, 16 Jun 2020 09:39:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:39:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:39:49: 14000000 INFO @ Tue, 16 Jun 2020 09:39:55: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:40:00: 16000000 INFO @ Tue, 16 Jun 2020 09:40:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:40:06: 17000000 INFO @ Tue, 16 Jun 2020 09:40:11: 18000000 INFO @ Tue, 16 Jun 2020 09:40:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4996808/SRX4996808.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:40:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4996808/SRX4996808.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:40:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4996808/SRX4996808.10_summits.bed INFO @ Tue, 16 Jun 2020 09:40:13: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (343 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:40:17: 19000000 INFO @ Tue, 16 Jun 2020 09:40:22: 20000000 INFO @ Tue, 16 Jun 2020 09:40:28: 21000000 INFO @ Tue, 16 Jun 2020 09:40:30: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:40:30: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:40:30: #1 total tags in treatment: 9382997 INFO @ Tue, 16 Jun 2020 09:40:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:40:30: #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 09:40:30: #1 tags after filtering in treatment: 8653003 INFO @ Tue, 16 Jun 2020 09:40:30: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 16 Jun 2020 09:40:30: #1 finished! INFO @ Tue, 16 Jun 2020 09:40:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:40:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:40:31: #2 number of paired peaks: 566 WARNING @ Tue, 16 Jun 2020 09:40:31: Fewer paired peaks (566) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 566 pairs to build model! INFO @ Tue, 16 Jun 2020 09:40:31: start model_add_line... INFO @ Tue, 16 Jun 2020 09:40:31: start X-correlation... INFO @ Tue, 16 Jun 2020 09:40:31: end of X-cor INFO @ Tue, 16 Jun 2020 09:40:31: #2 finished! INFO @ Tue, 16 Jun 2020 09:40:31: #2 predicted fragment length is 147 bps INFO @ Tue, 16 Jun 2020 09:40:31: #2 alternative fragment length(s) may be 4,147 bps INFO @ Tue, 16 Jun 2020 09:40:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4996808/SRX4996808.20_model.r INFO @ Tue, 16 Jun 2020 09:40:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:40:31: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:40:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:40:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4996808/SRX4996808.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:40:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4996808/SRX4996808.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:40:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4996808/SRX4996808.20_summits.bed INFO @ Tue, 16 Jun 2020 09:40:57: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (227 records, 4 fields): 1 millis CompletedMACS2peakCalling