Job ID = 14159271 SRX = SRX8976713 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 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: 00:11:43 14404796 reads; of these: 14404796 (100.00%) were paired; of these: 223049 (1.55%) aligned concordantly 0 times 12304312 (85.42%) aligned concordantly exactly 1 time 1877435 (13.03%) aligned concordantly >1 times ---- 223049 pairs aligned concordantly 0 times; of these: 78388 (35.14%) aligned discordantly 1 time ---- 144661 pairs aligned 0 times concordantly or discordantly; of these: 289322 mates make up the pairs; of these: 188620 (65.19%) aligned 0 times 62815 (21.71%) aligned exactly 1 time 37887 (13.10%) aligned >1 times 99.35% overall alignment rate Time searching: 00:11:43 Overall time: 00:11:43 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 12 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] 205866 / 14242992 = 0.0145 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 @ Wed, 08 Dec 2021 20:52:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976713/SRX8976713.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976713/SRX8976713.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976713/SRX8976713.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976713/SRX8976713.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 @ Wed, 08 Dec 2021 20:52:10: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:52:10: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:52:15: 1000000 INFO @ Wed, 08 Dec 2021 20:52:20: 2000000 INFO @ Wed, 08 Dec 2021 20:52:25: 3000000 INFO @ Wed, 08 Dec 2021 20:52:30: 4000000 INFO @ Wed, 08 Dec 2021 20:52:35: 5000000 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 @ Wed, 08 Dec 2021 20:52:40: 6000000 INFO @ Wed, 08 Dec 2021 20:52:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976713/SRX8976713.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976713/SRX8976713.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976713/SRX8976713.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976713/SRX8976713.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 @ Wed, 08 Dec 2021 20:52:40: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:52:40: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:52:45: 7000000 INFO @ Wed, 08 Dec 2021 20:52:46: 1000000 INFO @ Wed, 08 Dec 2021 20:52:50: 8000000 INFO @ Wed, 08 Dec 2021 20:52:52: 2000000 INFO @ Wed, 08 Dec 2021 20:52:56: 9000000 INFO @ Wed, 08 Dec 2021 20:52:58: 3000000 INFO @ Wed, 08 Dec 2021 20:53:01: 10000000 INFO @ Wed, 08 Dec 2021 20:53:03: 4000000 INFO @ Wed, 08 Dec 2021 20:53:07: 11000000 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 @ Wed, 08 Dec 2021 20:53:09: 5000000 INFO @ Wed, 08 Dec 2021 20:53:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976713/SRX8976713.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976713/SRX8976713.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976713/SRX8976713.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976713/SRX8976713.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 @ Wed, 08 Dec 2021 20:53:10: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:53:10: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:53:12: 12000000 INFO @ Wed, 08 Dec 2021 20:53:15: 6000000 INFO @ Wed, 08 Dec 2021 20:53:15: 1000000 INFO @ Wed, 08 Dec 2021 20:53:18: 13000000 INFO @ Wed, 08 Dec 2021 20:53:21: 2000000 INFO @ Wed, 08 Dec 2021 20:53:21: 7000000 INFO @ Wed, 08 Dec 2021 20:53:23: 14000000 INFO @ Wed, 08 Dec 2021 20:53:26: 3000000 INFO @ Wed, 08 Dec 2021 20:53:27: 8000000 INFO @ Wed, 08 Dec 2021 20:53:29: 15000000 INFO @ Wed, 08 Dec 2021 20:53:32: 4000000 INFO @ Wed, 08 Dec 2021 20:53:33: 9000000 INFO @ Wed, 08 Dec 2021 20:53:34: 16000000 INFO @ Wed, 08 Dec 2021 20:53:37: 5000000 INFO @ Wed, 08 Dec 2021 20:53:39: 10000000 INFO @ Wed, 08 Dec 2021 20:53:40: 17000000 INFO @ Wed, 08 Dec 2021 20:53:43: 6000000 INFO @ Wed, 08 Dec 2021 20:53:45: 11000000 INFO @ Wed, 08 Dec 2021 20:53:47: 18000000 INFO @ Wed, 08 Dec 2021 20:53:49: 7000000 INFO @ Wed, 08 Dec 2021 20:53:51: 12000000 INFO @ Wed, 08 Dec 2021 20:53:52: 19000000 INFO @ Wed, 08 Dec 2021 20:53:54: 8000000 INFO @ Wed, 08 Dec 2021 20:53:57: 13000000 INFO @ Wed, 08 Dec 2021 20:53:57: 20000000 INFO @ Wed, 08 Dec 2021 20:54:00: 9000000 INFO @ Wed, 08 Dec 2021 20:54:03: 14000000 INFO @ Wed, 08 Dec 2021 20:54:03: 21000000 INFO @ Wed, 08 Dec 2021 20:54:05: 10000000 INFO @ Wed, 08 Dec 2021 20:54:08: 22000000 INFO @ Wed, 08 Dec 2021 20:54:09: 15000000 INFO @ Wed, 08 Dec 2021 20:54:10: 11000000 INFO @ Wed, 08 Dec 2021 20:54:14: 23000000 INFO @ Wed, 08 Dec 2021 20:54:15: 16000000 INFO @ Wed, 08 Dec 2021 20:54:16: 12000000 INFO @ Wed, 08 Dec 2021 20:54:19: 24000000 INFO @ Wed, 08 Dec 2021 20:54:20: 17000000 INFO @ Wed, 08 Dec 2021 20:54:21: 13000000 INFO @ Wed, 08 Dec 2021 20:54:25: 25000000 INFO @ Wed, 08 Dec 2021 20:54:26: 18000000 INFO @ Wed, 08 Dec 2021 20:54:27: 14000000 INFO @ Wed, 08 Dec 2021 20:54:30: 26000000 INFO @ Wed, 08 Dec 2021 20:54:32: 15000000 INFO @ Wed, 08 Dec 2021 20:54:32: 19000000 INFO @ Wed, 08 Dec 2021 20:54:36: 27000000 INFO @ Wed, 08 Dec 2021 20:54:38: 16000000 INFO @ Wed, 08 Dec 2021 20:54:38: 20000000 INFO @ Wed, 08 Dec 2021 20:54:41: 28000000 INFO @ Wed, 08 Dec 2021 20:54:42: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:54:42: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:54:42: #1 total tags in treatment: 13976455 INFO @ Wed, 08 Dec 2021 20:54:42: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:54:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 20:54:42: #1 tags after filtering in treatment: 13039977 INFO @ Wed, 08 Dec 2021 20:54:42: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 20:54:42: #1 finished! INFO @ Wed, 08 Dec 2021 20:54:42: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:54:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:54:43: 17000000 INFO @ Wed, 08 Dec 2021 20:54:43: #2 number of paired peaks: 304 WARNING @ Wed, 08 Dec 2021 20:54:43: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Wed, 08 Dec 2021 20:54:43: start model_add_line... INFO @ Wed, 08 Dec 2021 20:54:43: start X-correlation... INFO @ Wed, 08 Dec 2021 20:54:43: end of X-cor INFO @ Wed, 08 Dec 2021 20:54:43: #2 finished! INFO @ Wed, 08 Dec 2021 20:54:43: #2 predicted fragment length is 156 bps INFO @ Wed, 08 Dec 2021 20:54:43: #2 alternative fragment length(s) may be 4,156 bps INFO @ Wed, 08 Dec 2021 20:54:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976713/SRX8976713.05_model.r INFO @ Wed, 08 Dec 2021 20:54:43: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:54:43: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:54:44: 21000000 INFO @ Wed, 08 Dec 2021 20:54:48: 18000000 INFO @ Wed, 08 Dec 2021 20:54:50: 22000000 INFO @ Wed, 08 Dec 2021 20:54:54: 19000000 INFO @ Wed, 08 Dec 2021 20:54:56: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 20:54:59: 20000000 INFO @ Wed, 08 Dec 2021 20:55:02: 24000000 INFO @ Wed, 08 Dec 2021 20:55:04: 21000000 INFO @ Wed, 08 Dec 2021 20:55:08: 25000000 INFO @ Wed, 08 Dec 2021 20:55:08: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:55:10: 22000000 INFO @ Wed, 08 Dec 2021 20:55:13: 26000000 INFO @ Wed, 08 Dec 2021 20:55:15: 23000000 INFO @ Wed, 08 Dec 2021 20:55:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976713/SRX8976713.05_peaks.xls INFO @ Wed, 08 Dec 2021 20:55:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976713/SRX8976713.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:55:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976713/SRX8976713.05_summits.bed INFO @ Wed, 08 Dec 2021 20:55:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (347 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:55:19: 27000000 INFO @ Wed, 08 Dec 2021 20:55:20: 24000000 INFO @ Wed, 08 Dec 2021 20:55:25: 28000000 INFO @ Wed, 08 Dec 2021 20:55:26: 25000000 INFO @ Wed, 08 Dec 2021 20:55:26: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:55:26: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:55:26: #1 total tags in treatment: 13976455 INFO @ Wed, 08 Dec 2021 20:55:26: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:55:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 20:55:27: #1 tags after filtering in treatment: 13039977 INFO @ Wed, 08 Dec 2021 20:55:27: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 20:55:27: #1 finished! INFO @ Wed, 08 Dec 2021 20:55:27: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:55:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:55:27: #2 number of paired peaks: 304 WARNING @ Wed, 08 Dec 2021 20:55:27: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Wed, 08 Dec 2021 20:55:27: start model_add_line... INFO @ Wed, 08 Dec 2021 20:55:27: start X-correlation... INFO @ Wed, 08 Dec 2021 20:55:28: end of X-cor INFO @ Wed, 08 Dec 2021 20:55:28: #2 finished! INFO @ Wed, 08 Dec 2021 20:55:28: #2 predicted fragment length is 156 bps INFO @ Wed, 08 Dec 2021 20:55:28: #2 alternative fragment length(s) may be 4,156 bps INFO @ Wed, 08 Dec 2021 20:55:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976713/SRX8976713.10_model.r INFO @ Wed, 08 Dec 2021 20:55:28: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:55:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:55:31: 26000000 INFO @ Wed, 08 Dec 2021 20:55:37: 27000000 INFO @ Wed, 08 Dec 2021 20:55:43: 28000000 INFO @ Wed, 08 Dec 2021 20:55:44: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:55:44: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:55:44: #1 total tags in treatment: 13976455 INFO @ Wed, 08 Dec 2021 20:55:44: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:55:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 20:55:45: #1 tags after filtering in treatment: 13039977 INFO @ Wed, 08 Dec 2021 20:55:45: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 20:55:45: #1 finished! INFO @ Wed, 08 Dec 2021 20:55:45: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:55:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:55:46: #2 number of paired peaks: 304 WARNING @ Wed, 08 Dec 2021 20:55:46: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Wed, 08 Dec 2021 20:55:46: start model_add_line... INFO @ Wed, 08 Dec 2021 20:55:46: start X-correlation... INFO @ Wed, 08 Dec 2021 20:55:46: end of X-cor INFO @ Wed, 08 Dec 2021 20:55:46: #2 finished! INFO @ Wed, 08 Dec 2021 20:55:46: #2 predicted fragment length is 156 bps INFO @ Wed, 08 Dec 2021 20:55:46: #2 alternative fragment length(s) may be 4,156 bps INFO @ Wed, 08 Dec 2021 20:55:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976713/SRX8976713.20_model.r INFO @ Wed, 08 Dec 2021 20:55:46: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:55:46: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:55:52: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 20:56:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976713/SRX8976713.10_peaks.xls INFO @ Wed, 08 Dec 2021 20:56:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976713/SRX8976713.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:56:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976713/SRX8976713.10_summits.bed INFO @ Wed, 08 Dec 2021 20:56:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (265 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:56:10: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:56:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976713/SRX8976713.20_peaks.xls INFO @ Wed, 08 Dec 2021 20:56:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976713/SRX8976713.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:56:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976713/SRX8976713.20_summits.bed INFO @ Wed, 08 Dec 2021 20:56:21: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (188 records, 4 fields): 2 millis CompletedMACS2peakCalling