Job ID = 14159321 SRX = SRX8976726 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: 00:10:33 14196394 reads; of these: 14196394 (100.00%) were paired; of these: 357223 (2.52%) aligned concordantly 0 times 11996976 (84.51%) aligned concordantly exactly 1 time 1842195 (12.98%) aligned concordantly >1 times ---- 357223 pairs aligned concordantly 0 times; of these: 178339 (49.92%) aligned discordantly 1 time ---- 178884 pairs aligned 0 times concordantly or discordantly; of these: 357768 mates make up the pairs; of these: 166194 (46.45%) aligned 0 times 112633 (31.48%) aligned exactly 1 time 78941 (22.06%) aligned >1 times 99.41% overall alignment rate Time searching: 00:10:33 Overall time: 00:10:33 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] 396612 / 13976370 = 0.0284 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 21:12:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976726/SRX8976726.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976726/SRX8976726.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976726/SRX8976726.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976726/SRX8976726.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 21:12:42: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:12:42: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:12:47: 1000000 INFO @ Wed, 08 Dec 2021 21:12:51: 2000000 INFO @ Wed, 08 Dec 2021 21:12:56: 3000000 INFO @ Wed, 08 Dec 2021 21:13:01: 4000000 INFO @ Wed, 08 Dec 2021 21:13:05: 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 21:13:10: 6000000 INFO @ Wed, 08 Dec 2021 21:13:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976726/SRX8976726.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976726/SRX8976726.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976726/SRX8976726.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976726/SRX8976726.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 21:13:12: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:13:12: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:13:16: 7000000 INFO @ Wed, 08 Dec 2021 21:13:19: 1000000 INFO @ Wed, 08 Dec 2021 21:13:21: 8000000 INFO @ Wed, 08 Dec 2021 21:13:26: 2000000 INFO @ Wed, 08 Dec 2021 21:13:27: 9000000 INFO @ Wed, 08 Dec 2021 21:13:32: 3000000 INFO @ Wed, 08 Dec 2021 21:13:33: 10000000 INFO @ Wed, 08 Dec 2021 21:13:39: 4000000 INFO @ Wed, 08 Dec 2021 21:13:39: 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 21:13:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976726/SRX8976726.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976726/SRX8976726.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976726/SRX8976726.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976726/SRX8976726.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 21:13:42: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:13:42: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:13:45: 12000000 INFO @ Wed, 08 Dec 2021 21:13:45: 5000000 INFO @ Wed, 08 Dec 2021 21:13:48: 1000000 INFO @ Wed, 08 Dec 2021 21:13:51: 13000000 INFO @ Wed, 08 Dec 2021 21:13:52: 6000000 INFO @ Wed, 08 Dec 2021 21:13:54: 2000000 INFO @ Wed, 08 Dec 2021 21:13:56: 14000000 INFO @ Wed, 08 Dec 2021 21:13:59: 7000000 INFO @ Wed, 08 Dec 2021 21:13:59: 3000000 INFO @ Wed, 08 Dec 2021 21:14:02: 15000000 INFO @ Wed, 08 Dec 2021 21:14:05: 8000000 INFO @ Wed, 08 Dec 2021 21:14:05: 4000000 INFO @ Wed, 08 Dec 2021 21:14:08: 16000000 INFO @ Wed, 08 Dec 2021 21:14:11: 5000000 INFO @ Wed, 08 Dec 2021 21:14:12: 9000000 INFO @ Wed, 08 Dec 2021 21:14:14: 17000000 INFO @ Wed, 08 Dec 2021 21:14:17: 6000000 INFO @ Wed, 08 Dec 2021 21:14:19: 10000000 INFO @ Wed, 08 Dec 2021 21:14:20: 18000000 INFO @ Wed, 08 Dec 2021 21:14:23: 7000000 INFO @ Wed, 08 Dec 2021 21:14:26: 11000000 INFO @ Wed, 08 Dec 2021 21:14:26: 19000000 INFO @ Wed, 08 Dec 2021 21:14:29: 8000000 INFO @ Wed, 08 Dec 2021 21:14:32: 20000000 INFO @ Wed, 08 Dec 2021 21:14:33: 12000000 INFO @ Wed, 08 Dec 2021 21:14:35: 9000000 INFO @ Wed, 08 Dec 2021 21:14:38: 21000000 INFO @ Wed, 08 Dec 2021 21:14:39: 13000000 INFO @ Wed, 08 Dec 2021 21:14:40: 10000000 INFO @ Wed, 08 Dec 2021 21:14:43: 22000000 INFO @ Wed, 08 Dec 2021 21:14:46: 14000000 INFO @ Wed, 08 Dec 2021 21:14:46: 11000000 INFO @ Wed, 08 Dec 2021 21:14:49: 23000000 INFO @ Wed, 08 Dec 2021 21:14:52: 12000000 INFO @ Wed, 08 Dec 2021 21:14:53: 15000000 INFO @ Wed, 08 Dec 2021 21:14:55: 24000000 INFO @ Wed, 08 Dec 2021 21:14:58: 13000000 INFO @ Wed, 08 Dec 2021 21:15:00: 16000000 INFO @ Wed, 08 Dec 2021 21:15:01: 25000000 INFO @ Wed, 08 Dec 2021 21:15:04: 14000000 INFO @ Wed, 08 Dec 2021 21:15:07: 17000000 INFO @ Wed, 08 Dec 2021 21:15:07: 26000000 INFO @ Wed, 08 Dec 2021 21:15:10: 15000000 INFO @ Wed, 08 Dec 2021 21:15:13: 27000000 INFO @ Wed, 08 Dec 2021 21:15:14: 18000000 INFO @ Wed, 08 Dec 2021 21:15:15: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:15:15: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:15:15: #1 total tags in treatment: 13445466 INFO @ Wed, 08 Dec 2021 21:15:15: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:15:15: #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 21:15:15: #1 tags after filtering in treatment: 12540704 INFO @ Wed, 08 Dec 2021 21:15:15: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 21:15:15: #1 finished! INFO @ Wed, 08 Dec 2021 21:15:15: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:15:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:15:16: 16000000 INFO @ Wed, 08 Dec 2021 21:15:16: #2 number of paired peaks: 321 WARNING @ Wed, 08 Dec 2021 21:15:16: Fewer paired peaks (321) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 321 pairs to build model! INFO @ Wed, 08 Dec 2021 21:15:16: start model_add_line... INFO @ Wed, 08 Dec 2021 21:15:16: start X-correlation... INFO @ Wed, 08 Dec 2021 21:15:16: end of X-cor INFO @ Wed, 08 Dec 2021 21:15:16: #2 finished! INFO @ Wed, 08 Dec 2021 21:15:16: #2 predicted fragment length is 164 bps INFO @ Wed, 08 Dec 2021 21:15:16: #2 alternative fragment length(s) may be 4,136,164 bps INFO @ Wed, 08 Dec 2021 21:15:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976726/SRX8976726.05_model.r INFO @ Wed, 08 Dec 2021 21:15:16: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:15:16: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:15:20: 19000000 INFO @ Wed, 08 Dec 2021 21:15:21: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 21:15:27: 20000000 INFO @ Wed, 08 Dec 2021 21:15:27: 18000000 INFO @ Wed, 08 Dec 2021 21:15:33: 19000000 INFO @ Wed, 08 Dec 2021 21:15:34: 21000000 INFO @ Wed, 08 Dec 2021 21:15:39: 20000000 INFO @ Wed, 08 Dec 2021 21:15:40: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:15:41: 22000000 INFO @ Wed, 08 Dec 2021 21:15:45: 21000000 INFO @ Wed, 08 Dec 2021 21:15:47: 23000000 INFO @ Wed, 08 Dec 2021 21:15:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976726/SRX8976726.05_peaks.xls INFO @ Wed, 08 Dec 2021 21:15:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976726/SRX8976726.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:15:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976726/SRX8976726.05_summits.bed INFO @ Wed, 08 Dec 2021 21:15:50: Done! INFO @ Wed, 08 Dec 2021 21:15:50: 22000000 pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (319 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:15:53: 24000000 INFO @ Wed, 08 Dec 2021 21:15:56: 23000000 INFO @ Wed, 08 Dec 2021 21:16:00: 25000000 INFO @ Wed, 08 Dec 2021 21:16:02: 24000000 INFO @ Wed, 08 Dec 2021 21:16:07: 26000000 INFO @ Wed, 08 Dec 2021 21:16:08: 25000000 INFO @ Wed, 08 Dec 2021 21:16:13: 27000000 INFO @ Wed, 08 Dec 2021 21:16:14: 26000000 INFO @ Wed, 08 Dec 2021 21:16:16: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:16:16: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:16:16: #1 total tags in treatment: 13445466 INFO @ Wed, 08 Dec 2021 21:16:16: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:16:16: #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 21:16:16: #1 tags after filtering in treatment: 12540704 INFO @ Wed, 08 Dec 2021 21:16:16: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 21:16:16: #1 finished! INFO @ Wed, 08 Dec 2021 21:16:16: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:16:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:16:17: #2 number of paired peaks: 321 WARNING @ Wed, 08 Dec 2021 21:16:17: Fewer paired peaks (321) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 321 pairs to build model! INFO @ Wed, 08 Dec 2021 21:16:17: start model_add_line... INFO @ Wed, 08 Dec 2021 21:16:17: start X-correlation... INFO @ Wed, 08 Dec 2021 21:16:17: end of X-cor INFO @ Wed, 08 Dec 2021 21:16:17: #2 finished! INFO @ Wed, 08 Dec 2021 21:16:17: #2 predicted fragment length is 164 bps INFO @ Wed, 08 Dec 2021 21:16:17: #2 alternative fragment length(s) may be 4,136,164 bps INFO @ Wed, 08 Dec 2021 21:16:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976726/SRX8976726.10_model.r INFO @ Wed, 08 Dec 2021 21:16:17: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:16:17: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 21:16:19: 27000000 INFO @ Wed, 08 Dec 2021 21:16:21: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:16:21: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:16:21: #1 total tags in treatment: 13445466 INFO @ Wed, 08 Dec 2021 21:16:21: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:16:21: #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 21:16:22: #1 tags after filtering in treatment: 12540704 INFO @ Wed, 08 Dec 2021 21:16:22: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 21:16:22: #1 finished! INFO @ Wed, 08 Dec 2021 21:16:22: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:16:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:16:22: #2 number of paired peaks: 321 WARNING @ Wed, 08 Dec 2021 21:16:22: Fewer paired peaks (321) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 321 pairs to build model! INFO @ Wed, 08 Dec 2021 21:16:22: start model_add_line... INFO @ Wed, 08 Dec 2021 21:16:23: start X-correlation... INFO @ Wed, 08 Dec 2021 21:16:23: end of X-cor INFO @ Wed, 08 Dec 2021 21:16:23: #2 finished! INFO @ Wed, 08 Dec 2021 21:16:23: #2 predicted fragment length is 164 bps INFO @ Wed, 08 Dec 2021 21:16:23: #2 alternative fragment length(s) may be 4,136,164 bps INFO @ Wed, 08 Dec 2021 21:16:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976726/SRX8976726.20_model.r INFO @ Wed, 08 Dec 2021 21:16:23: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:16:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:16:41: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:16:47: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:16:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976726/SRX8976726.10_peaks.xls INFO @ Wed, 08 Dec 2021 21:16:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976726/SRX8976726.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:16:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976726/SRX8976726.10_summits.bed INFO @ Wed, 08 Dec 2021 21:16:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (240 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:16:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976726/SRX8976726.20_peaks.xls INFO @ Wed, 08 Dec 2021 21:16:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976726/SRX8976726.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:16:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976726/SRX8976726.20_summits.bed INFO @ Wed, 08 Dec 2021 21:16:57: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (163 records, 4 fields): 2 millis CompletedMACS2peakCalling