Job ID = 14159280 SRX = SRX8976715 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: 00:11:26 14285287 reads; of these: 14285287 (100.00%) were paired; of these: 229927 (1.61%) aligned concordantly 0 times 12190314 (85.33%) aligned concordantly exactly 1 time 1865046 (13.06%) aligned concordantly >1 times ---- 229927 pairs aligned concordantly 0 times; of these: 90050 (39.16%) aligned discordantly 1 time ---- 139877 pairs aligned 0 times concordantly or discordantly; of these: 279754 mates make up the pairs; of these: 174740 (62.46%) aligned 0 times 64914 (23.20%) aligned exactly 1 time 40100 (14.33%) aligned >1 times 99.39% overall alignment rate Time searching: 00:11:26 Overall time: 00:11:26 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] 181863 / 14130244 = 0.0129 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 20:54:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976715/SRX8976715.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976715/SRX8976715.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976715/SRX8976715.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976715/SRX8976715.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 20:54:31: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:54:31: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:54:37: 1000000 INFO @ Wed, 08 Dec 2021 20:54:44: 2000000 INFO @ Wed, 08 Dec 2021 20:54:50: 3000000 INFO @ Wed, 08 Dec 2021 20:54:56: 4000000 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 20:55:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976715/SRX8976715.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976715/SRX8976715.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976715/SRX8976715.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976715/SRX8976715.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 20:55:01: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:55:01: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:55:03: 5000000 INFO @ Wed, 08 Dec 2021 20:55:07: 1000000 INFO @ Wed, 08 Dec 2021 20:55:10: 6000000 INFO @ Wed, 08 Dec 2021 20:55:14: 2000000 INFO @ Wed, 08 Dec 2021 20:55:17: 7000000 INFO @ Wed, 08 Dec 2021 20:55:20: 3000000 INFO @ Wed, 08 Dec 2021 20:55:25: 8000000 INFO @ Wed, 08 Dec 2021 20:55:27: 4000000 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 20:55:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976715/SRX8976715.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976715/SRX8976715.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976715/SRX8976715.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976715/SRX8976715.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 20:55:30: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:55:30: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:55:32: 9000000 INFO @ Wed, 08 Dec 2021 20:55:34: 5000000 INFO @ Wed, 08 Dec 2021 20:55:37: 1000000 INFO @ Wed, 08 Dec 2021 20:55:39: 10000000 INFO @ Wed, 08 Dec 2021 20:55:40: 6000000 INFO @ Wed, 08 Dec 2021 20:55:44: 2000000 INFO @ Wed, 08 Dec 2021 20:55:46: 11000000 INFO @ Wed, 08 Dec 2021 20:55:47: 7000000 INFO @ Wed, 08 Dec 2021 20:55:51: 3000000 INFO @ Wed, 08 Dec 2021 20:55:54: 12000000 INFO @ Wed, 08 Dec 2021 20:55:54: 8000000 INFO @ Wed, 08 Dec 2021 20:55:58: 4000000 INFO @ Wed, 08 Dec 2021 20:56:01: 9000000 INFO @ Wed, 08 Dec 2021 20:56:01: 13000000 INFO @ Wed, 08 Dec 2021 20:56:05: 5000000 INFO @ Wed, 08 Dec 2021 20:56:07: 10000000 INFO @ Wed, 08 Dec 2021 20:56:08: 14000000 INFO @ Wed, 08 Dec 2021 20:56:11: 6000000 INFO @ Wed, 08 Dec 2021 20:56:14: 11000000 INFO @ Wed, 08 Dec 2021 20:56:16: 15000000 INFO @ Wed, 08 Dec 2021 20:56:18: 7000000 INFO @ Wed, 08 Dec 2021 20:56:21: 12000000 INFO @ Wed, 08 Dec 2021 20:56:23: 16000000 INFO @ Wed, 08 Dec 2021 20:56:25: 8000000 INFO @ Wed, 08 Dec 2021 20:56:28: 13000000 INFO @ Wed, 08 Dec 2021 20:56:30: 17000000 INFO @ Wed, 08 Dec 2021 20:56:32: 9000000 INFO @ Wed, 08 Dec 2021 20:56:34: 14000000 INFO @ Wed, 08 Dec 2021 20:56:38: 18000000 INFO @ Wed, 08 Dec 2021 20:56:39: 10000000 INFO @ Wed, 08 Dec 2021 20:56:41: 15000000 INFO @ Wed, 08 Dec 2021 20:56:45: 19000000 INFO @ Wed, 08 Dec 2021 20:56:45: 11000000 INFO @ Wed, 08 Dec 2021 20:56:48: 16000000 INFO @ Wed, 08 Dec 2021 20:56:52: 12000000 INFO @ Wed, 08 Dec 2021 20:56:52: 20000000 INFO @ Wed, 08 Dec 2021 20:56:54: 17000000 INFO @ Wed, 08 Dec 2021 20:56:59: 13000000 INFO @ Wed, 08 Dec 2021 20:57:00: 21000000 INFO @ Wed, 08 Dec 2021 20:57:01: 18000000 INFO @ Wed, 08 Dec 2021 20:57:06: 14000000 INFO @ Wed, 08 Dec 2021 20:57:07: 22000000 INFO @ Wed, 08 Dec 2021 20:57:08: 19000000 INFO @ Wed, 08 Dec 2021 20:57:13: 15000000 INFO @ Wed, 08 Dec 2021 20:57:14: 20000000 INFO @ Wed, 08 Dec 2021 20:57:15: 23000000 INFO @ Wed, 08 Dec 2021 20:57:20: 16000000 INFO @ Wed, 08 Dec 2021 20:57:21: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 20:57:22: 24000000 INFO @ Wed, 08 Dec 2021 20:57:26: 17000000 INFO @ Wed, 08 Dec 2021 20:57:28: 22000000 INFO @ Wed, 08 Dec 2021 20:57:29: 25000000 INFO @ Wed, 08 Dec 2021 20:57:33: 18000000 INFO @ Wed, 08 Dec 2021 20:57:35: 23000000 INFO @ Wed, 08 Dec 2021 20:57:37: 26000000 INFO @ Wed, 08 Dec 2021 20:57:40: 19000000 INFO @ Wed, 08 Dec 2021 20:57:42: 24000000 INFO @ Wed, 08 Dec 2021 20:57:44: 27000000 INFO @ Wed, 08 Dec 2021 20:57:47: 20000000 INFO @ Wed, 08 Dec 2021 20:57:48: 25000000 INFO @ Wed, 08 Dec 2021 20:57:52: 28000000 INFO @ Wed, 08 Dec 2021 20:57:52: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:57:52: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:57:52: #1 total tags in treatment: 13874075 INFO @ Wed, 08 Dec 2021 20:57:52: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:57:52: #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 20:57:52: #1 tags after filtering in treatment: 12961292 INFO @ Wed, 08 Dec 2021 20:57:52: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 20:57:52: #1 finished! INFO @ Wed, 08 Dec 2021 20:57:52: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:57:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:57:53: #2 number of paired peaks: 321 WARNING @ Wed, 08 Dec 2021 20:57:53: 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 20:57:53: start model_add_line... INFO @ Wed, 08 Dec 2021 20:57:53: start X-correlation... INFO @ Wed, 08 Dec 2021 20:57:53: end of X-cor INFO @ Wed, 08 Dec 2021 20:57:53: #2 finished! INFO @ Wed, 08 Dec 2021 20:57:53: #2 predicted fragment length is 138 bps INFO @ Wed, 08 Dec 2021 20:57:53: #2 alternative fragment length(s) may be 4,138,147 bps INFO @ Wed, 08 Dec 2021 20:57:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976715/SRX8976715.05_model.r INFO @ Wed, 08 Dec 2021 20:57:53: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:57:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:57:53: 21000000 INFO @ Wed, 08 Dec 2021 20:57:55: 26000000 INFO @ Wed, 08 Dec 2021 20:58:00: 22000000 INFO @ Wed, 08 Dec 2021 20:58:01: 27000000 INFO @ Wed, 08 Dec 2021 20:58:06: 23000000 INFO @ Wed, 08 Dec 2021 20:58:07: 28000000 INFO @ Wed, 08 Dec 2021 20:58:07: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:58:07: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:58:07: #1 total tags in treatment: 13874075 INFO @ Wed, 08 Dec 2021 20:58:07: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:58:07: #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 20:58:07: #1 tags after filtering in treatment: 12961292 INFO @ Wed, 08 Dec 2021 20:58:07: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 20:58:07: #1 finished! INFO @ Wed, 08 Dec 2021 20:58:07: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:58:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:58:08: #2 number of paired peaks: 321 WARNING @ Wed, 08 Dec 2021 20:58:08: 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 20:58:08: start model_add_line... INFO @ Wed, 08 Dec 2021 20:58:08: start X-correlation... INFO @ Wed, 08 Dec 2021 20:58:08: end of X-cor INFO @ Wed, 08 Dec 2021 20:58:08: #2 finished! INFO @ Wed, 08 Dec 2021 20:58:08: #2 predicted fragment length is 138 bps INFO @ Wed, 08 Dec 2021 20:58:08: #2 alternative fragment length(s) may be 4,138,147 bps INFO @ Wed, 08 Dec 2021 20:58:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976715/SRX8976715.10_model.r INFO @ Wed, 08 Dec 2021 20:58:08: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:58:08: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:58:12: 24000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 20:58:17: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:58:17: 25000000 INFO @ Wed, 08 Dec 2021 20:58:22: 26000000 INFO @ Wed, 08 Dec 2021 20:58:28: 27000000 INFO @ Wed, 08 Dec 2021 20:58:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976715/SRX8976715.05_peaks.xls INFO @ Wed, 08 Dec 2021 20:58:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976715/SRX8976715.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:58:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976715/SRX8976715.05_summits.bed INFO @ Wed, 08 Dec 2021 20:58:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (368 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:58:32: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:58:33: 28000000 INFO @ Wed, 08 Dec 2021 20:58:33: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:58:33: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:58:33: #1 total tags in treatment: 13874075 INFO @ Wed, 08 Dec 2021 20:58:33: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:58:33: #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 20:58:33: #1 tags after filtering in treatment: 12961292 INFO @ Wed, 08 Dec 2021 20:58:33: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 20:58:33: #1 finished! INFO @ Wed, 08 Dec 2021 20:58:33: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:58:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:58:34: #2 number of paired peaks: 321 WARNING @ Wed, 08 Dec 2021 20:58:34: 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 20:58:34: start model_add_line... INFO @ Wed, 08 Dec 2021 20:58:34: start X-correlation... INFO @ Wed, 08 Dec 2021 20:58:34: end of X-cor INFO @ Wed, 08 Dec 2021 20:58:34: #2 finished! INFO @ Wed, 08 Dec 2021 20:58:34: #2 predicted fragment length is 138 bps INFO @ Wed, 08 Dec 2021 20:58:34: #2 alternative fragment length(s) may be 4,138,147 bps INFO @ Wed, 08 Dec 2021 20:58:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976715/SRX8976715.20_model.r INFO @ Wed, 08 Dec 2021 20:58:34: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:58:34: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:58:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976715/SRX8976715.10_peaks.xls INFO @ Wed, 08 Dec 2021 20:58:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976715/SRX8976715.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:58:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976715/SRX8976715.10_summits.bed INFO @ Wed, 08 Dec 2021 20:58:43: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (270 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:58:57: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:59:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976715/SRX8976715.20_peaks.xls INFO @ Wed, 08 Dec 2021 20:59:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976715/SRX8976715.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:59:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976715/SRX8976715.20_summits.bed INFO @ Wed, 08 Dec 2021 20:59:09: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (192 records, 4 fields): 2 millis CompletedMACS2peakCalling