Job ID = 14159325 SRX = SRX8976730 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: 00:11:46 13539102 reads; of these: 13539102 (100.00%) were paired; of these: 926423 (6.84%) aligned concordantly 0 times 10985633 (81.14%) aligned concordantly exactly 1 time 1627046 (12.02%) aligned concordantly >1 times ---- 926423 pairs aligned concordantly 0 times; of these: 657975 (71.02%) aligned discordantly 1 time ---- 268448 pairs aligned 0 times concordantly or discordantly; of these: 536896 mates make up the pairs; of these: 172335 (32.10%) aligned 0 times 176442 (32.86%) aligned exactly 1 time 188119 (35.04%) aligned >1 times 99.36% overall alignment rate Time searching: 00:11:46 Overall time: 00:11:46 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] 370470 / 13239798 = 0.0280 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 21:17:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976730/SRX8976730.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976730/SRX8976730.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976730/SRX8976730.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976730/SRX8976730.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 21:17:19: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:17:19: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:17:24: 1000000 INFO @ Wed, 08 Dec 2021 21:17:27: 2000000 INFO @ Wed, 08 Dec 2021 21:17:31: 3000000 INFO @ Wed, 08 Dec 2021 21:17:35: 4000000 INFO @ Wed, 08 Dec 2021 21:17:40: 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 21:17:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976730/SRX8976730.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976730/SRX8976730.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976730/SRX8976730.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976730/SRX8976730.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 21:17:43: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:17:43: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:17:44: 6000000 INFO @ Wed, 08 Dec 2021 21:17:47: 1000000 INFO @ Wed, 08 Dec 2021 21:17:48: 7000000 INFO @ Wed, 08 Dec 2021 21:17:51: 2000000 INFO @ Wed, 08 Dec 2021 21:17:53: 8000000 INFO @ Wed, 08 Dec 2021 21:17:55: 3000000 INFO @ Wed, 08 Dec 2021 21:17:57: 9000000 INFO @ Wed, 08 Dec 2021 21:18:00: 4000000 INFO @ Wed, 08 Dec 2021 21:18:01: 10000000 INFO @ Wed, 08 Dec 2021 21:18:04: 5000000 INFO @ Wed, 08 Dec 2021 21:18:05: 11000000 INFO @ Wed, 08 Dec 2021 21:18:08: 6000000 INFO @ Wed, 08 Dec 2021 21:18:09: 12000000 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 21:18:12: 7000000 INFO @ Wed, 08 Dec 2021 21:18:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976730/SRX8976730.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976730/SRX8976730.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976730/SRX8976730.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976730/SRX8976730.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 21:18:13: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:18:13: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:18:13: 13000000 INFO @ Wed, 08 Dec 2021 21:18:17: 8000000 INFO @ Wed, 08 Dec 2021 21:18:17: 1000000 INFO @ Wed, 08 Dec 2021 21:18:18: 14000000 INFO @ Wed, 08 Dec 2021 21:18:21: 9000000 INFO @ Wed, 08 Dec 2021 21:18:21: 2000000 INFO @ Wed, 08 Dec 2021 21:18:22: 15000000 INFO @ Wed, 08 Dec 2021 21:18:25: 10000000 INFO @ Wed, 08 Dec 2021 21:18:25: 3000000 INFO @ Wed, 08 Dec 2021 21:18:26: 16000000 INFO @ Wed, 08 Dec 2021 21:18:29: 11000000 INFO @ Wed, 08 Dec 2021 21:18:30: 4000000 INFO @ Wed, 08 Dec 2021 21:18:30: 17000000 INFO @ Wed, 08 Dec 2021 21:18:33: 12000000 INFO @ Wed, 08 Dec 2021 21:18:34: 5000000 INFO @ Wed, 08 Dec 2021 21:18:34: 18000000 INFO @ Wed, 08 Dec 2021 21:18:38: 13000000 INFO @ Wed, 08 Dec 2021 21:18:38: 6000000 INFO @ Wed, 08 Dec 2021 21:18:38: 19000000 INFO @ Wed, 08 Dec 2021 21:18:42: 14000000 INFO @ Wed, 08 Dec 2021 21:18:42: 7000000 INFO @ Wed, 08 Dec 2021 21:18:43: 20000000 INFO @ Wed, 08 Dec 2021 21:18:46: 15000000 INFO @ Wed, 08 Dec 2021 21:18:47: 21000000 INFO @ Wed, 08 Dec 2021 21:18:47: 8000000 INFO @ Wed, 08 Dec 2021 21:18:51: 16000000 INFO @ Wed, 08 Dec 2021 21:18:51: 22000000 INFO @ Wed, 08 Dec 2021 21:18:51: 9000000 INFO @ Wed, 08 Dec 2021 21:18:55: 17000000 INFO @ Wed, 08 Dec 2021 21:18:55: 23000000 INFO @ Wed, 08 Dec 2021 21:18:56: 10000000 INFO @ Wed, 08 Dec 2021 21:18:59: 24000000 INFO @ Wed, 08 Dec 2021 21:19:00: 18000000 INFO @ Wed, 08 Dec 2021 21:19:00: 11000000 INFO @ Wed, 08 Dec 2021 21:19:04: 25000000 INFO @ Wed, 08 Dec 2021 21:19:04: 12000000 INFO @ Wed, 08 Dec 2021 21:19:04: 19000000 INFO @ Wed, 08 Dec 2021 21:19:08: 26000000 INFO @ Wed, 08 Dec 2021 21:19:08: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:19:08: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:19:08: #1 total tags in treatment: 12255847 INFO @ Wed, 08 Dec 2021 21:19:08: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:19:08: #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 21:19:09: 20000000 INFO @ Wed, 08 Dec 2021 21:19:09: #1 tags after filtering in treatment: 11472531 INFO @ Wed, 08 Dec 2021 21:19:09: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 21:19:09: #1 finished! INFO @ Wed, 08 Dec 2021 21:19:09: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:19:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:19:09: 13000000 INFO @ Wed, 08 Dec 2021 21:19:10: #2 number of paired peaks: 366 WARNING @ Wed, 08 Dec 2021 21:19:10: Fewer paired peaks (366) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 366 pairs to build model! INFO @ Wed, 08 Dec 2021 21:19:10: start model_add_line... INFO @ Wed, 08 Dec 2021 21:19:10: start X-correlation... INFO @ Wed, 08 Dec 2021 21:19:10: end of X-cor INFO @ Wed, 08 Dec 2021 21:19:10: #2 finished! INFO @ Wed, 08 Dec 2021 21:19:10: #2 predicted fragment length is 150 bps INFO @ Wed, 08 Dec 2021 21:19:10: #2 alternative fragment length(s) may be 4,124,150 bps INFO @ Wed, 08 Dec 2021 21:19:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976730/SRX8976730.05_model.r INFO @ Wed, 08 Dec 2021 21:19:10: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:19:10: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:19:13: 21000000 INFO @ Wed, 08 Dec 2021 21:19:13: 14000000 INFO @ Wed, 08 Dec 2021 21:19:17: 22000000 INFO @ Wed, 08 Dec 2021 21:19:18: 15000000 INFO @ Wed, 08 Dec 2021 21:19:22: 23000000 INFO @ Wed, 08 Dec 2021 21:19:22: 16000000 INFO @ Wed, 08 Dec 2021 21:19:26: 24000000 INFO @ Wed, 08 Dec 2021 21:19:27: 17000000 INFO @ Wed, 08 Dec 2021 21:19:30: 25000000 INFO @ Wed, 08 Dec 2021 21:19:31: 18000000 INFO @ Wed, 08 Dec 2021 21:19:32: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:19:34: 26000000 INFO @ Wed, 08 Dec 2021 21:19:35: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:19:35: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:19:35: #1 total tags in treatment: 12255847 INFO @ Wed, 08 Dec 2021 21:19:35: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:19:35: #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 21:19:35: 19000000 INFO @ Wed, 08 Dec 2021 21:19:35: #1 tags after filtering in treatment: 11472531 INFO @ Wed, 08 Dec 2021 21:19:35: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 21:19:35: #1 finished! INFO @ Wed, 08 Dec 2021 21:19:35: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:19:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:19:36: #2 number of paired peaks: 366 WARNING @ Wed, 08 Dec 2021 21:19:36: Fewer paired peaks (366) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 366 pairs to build model! INFO @ Wed, 08 Dec 2021 21:19:36: start model_add_line... INFO @ Wed, 08 Dec 2021 21:19:36: start X-correlation... INFO @ Wed, 08 Dec 2021 21:19:36: end of X-cor INFO @ Wed, 08 Dec 2021 21:19:36: #2 finished! INFO @ Wed, 08 Dec 2021 21:19:36: #2 predicted fragment length is 150 bps INFO @ Wed, 08 Dec 2021 21:19:36: #2 alternative fragment length(s) may be 4,124,150 bps INFO @ Wed, 08 Dec 2021 21:19:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976730/SRX8976730.10_model.r INFO @ Wed, 08 Dec 2021 21:19:36: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:19:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:19:40: 20000000 INFO @ Wed, 08 Dec 2021 21:19:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976730/SRX8976730.05_peaks.xls INFO @ Wed, 08 Dec 2021 21:19:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976730/SRX8976730.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:19:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976730/SRX8976730.05_summits.bed INFO @ Wed, 08 Dec 2021 21:19:42: Done! INFO @ Wed, 08 Dec 2021 21:19:44: 21000000 INFO @ Wed, 08 Dec 2021 21:19:49: 22000000 INFO @ Wed, 08 Dec 2021 21:19:53: 23000000 BedGraph に変換しました。 INFO @ Wed, 08 Dec 2021 21:19:57: 24000000 pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (345 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:19:58: #3 Call peaks for each chromosome... BigWig に変換中... INFO @ Wed, 08 Dec 2021 21:20:02: 25000000 INFO @ Wed, 08 Dec 2021 21:20:06: 26000000 INFO @ Wed, 08 Dec 2021 21:20:07: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:20:07: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:20:07: #1 total tags in treatment: 12255847 INFO @ Wed, 08 Dec 2021 21:20:07: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:20:07: #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 21:20:07: #1 tags after filtering in treatment: 11472531 INFO @ Wed, 08 Dec 2021 21:20:07: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 21:20:07: #1 finished! INFO @ Wed, 08 Dec 2021 21:20:07: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:20:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:20:08: #2 number of paired peaks: 366 WARNING @ Wed, 08 Dec 2021 21:20:08: Fewer paired peaks (366) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 366 pairs to build model! INFO @ Wed, 08 Dec 2021 21:20:08: start model_add_line... INFO @ Wed, 08 Dec 2021 21:20:08: start X-correlation... INFO @ Wed, 08 Dec 2021 21:20:08: end of X-cor INFO @ Wed, 08 Dec 2021 21:20:08: #2 finished! INFO @ Wed, 08 Dec 2021 21:20:08: #2 predicted fragment length is 150 bps INFO @ Wed, 08 Dec 2021 21:20:08: #2 alternative fragment length(s) may be 4,124,150 bps INFO @ Wed, 08 Dec 2021 21:20:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976730/SRX8976730.20_model.r INFO @ Wed, 08 Dec 2021 21:20:08: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:20:08: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:20:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976730/SRX8976730.10_peaks.xls INFO @ Wed, 08 Dec 2021 21:20:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976730/SRX8976730.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:20:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976730/SRX8976730.10_summits.bed INFO @ Wed, 08 Dec 2021 21:20:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (253 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:20:30: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:20:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976730/SRX8976730.20_peaks.xls INFO @ Wed, 08 Dec 2021 21:20:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976730/SRX8976730.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:20:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976730/SRX8976730.20_summits.bed INFO @ Wed, 08 Dec 2021 21:20:40: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (179 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。