Job ID = 14158914 SRX = SRX8976715 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14285287 spots for SRR12483319/SRR12483319.sra Written 14285287 spots for SRR12483319/SRR12483319.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159280 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:15:38 14285287 reads; of these: 14285287 (100.00%) were paired; of these: 230070 (1.61%) aligned concordantly 0 times 12190319 (85.33%) aligned concordantly exactly 1 time 1864898 (13.05%) aligned concordantly >1 times ---- 230070 pairs aligned concordantly 0 times; of these: 90034 (39.13%) aligned discordantly 1 time ---- 140036 pairs aligned 0 times concordantly or discordantly; of these: 280072 mates make up the pairs; of these: 175022 (62.49%) aligned 0 times 64938 (23.19%) aligned exactly 1 time 40112 (14.32%) aligned >1 times 99.39% overall alignment rate Time searching: 00:15:38 Overall time: 00:15:38 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] 181871 / 14130085 = 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 18:45:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976715/SRX8976715.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976715/SRX8976715.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976715/SRX8976715.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 18:45:13: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:45:13: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:45:24: 1000000 INFO @ Wed, 08 Dec 2021 18:45:35: 2000000 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 18:45:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976715/SRX8976715.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976715/SRX8976715.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976715/SRX8976715.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 18:45:43: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:45:43: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:45:46: 3000000 INFO @ Wed, 08 Dec 2021 18:45:52: 1000000 INFO @ Wed, 08 Dec 2021 18:45:56: 4000000 INFO @ Wed, 08 Dec 2021 18:46:01: 2000000 INFO @ Wed, 08 Dec 2021 18:46:06: 5000000 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 18:46:10: 3000000 INFO @ Wed, 08 Dec 2021 18:46:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976715/SRX8976715.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976715/SRX8976715.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976715/SRX8976715.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 18:46:13: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:46:13: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:46:16: 6000000 INFO @ Wed, 08 Dec 2021 18:46:19: 4000000 INFO @ Wed, 08 Dec 2021 18:46:23: 1000000 INFO @ Wed, 08 Dec 2021 18:46:26: 7000000 INFO @ Wed, 08 Dec 2021 18:46:28: 5000000 INFO @ Wed, 08 Dec 2021 18:46:34: 2000000 INFO @ Wed, 08 Dec 2021 18:46:36: 8000000 INFO @ Wed, 08 Dec 2021 18:46:37: 6000000 INFO @ Wed, 08 Dec 2021 18:46:44: 3000000 INFO @ Wed, 08 Dec 2021 18:46:46: 9000000 INFO @ Wed, 08 Dec 2021 18:46:46: 7000000 INFO @ Wed, 08 Dec 2021 18:46:55: 4000000 INFO @ Wed, 08 Dec 2021 18:46:55: 8000000 INFO @ Wed, 08 Dec 2021 18:46:57: 10000000 INFO @ Wed, 08 Dec 2021 18:47:04: 9000000 INFO @ Wed, 08 Dec 2021 18:47:05: 5000000 INFO @ Wed, 08 Dec 2021 18:47:07: 11000000 INFO @ Wed, 08 Dec 2021 18:47:13: 10000000 INFO @ Wed, 08 Dec 2021 18:47:15: 6000000 INFO @ Wed, 08 Dec 2021 18:47:18: 12000000 INFO @ Wed, 08 Dec 2021 18:47:22: 11000000 INFO @ Wed, 08 Dec 2021 18:47:25: 7000000 INFO @ Wed, 08 Dec 2021 18:47:29: 13000000 INFO @ Wed, 08 Dec 2021 18:47:31: 12000000 INFO @ Wed, 08 Dec 2021 18:47:35: 8000000 INFO @ Wed, 08 Dec 2021 18:47:39: 14000000 INFO @ Wed, 08 Dec 2021 18:47:40: 13000000 INFO @ Wed, 08 Dec 2021 18:47:46: 9000000 INFO @ Wed, 08 Dec 2021 18:47:49: 14000000 INFO @ Wed, 08 Dec 2021 18:47:50: 15000000 INFO @ Wed, 08 Dec 2021 18:47:57: 10000000 INFO @ Wed, 08 Dec 2021 18:47:58: 15000000 INFO @ Wed, 08 Dec 2021 18:48:00: 16000000 INFO @ Wed, 08 Dec 2021 18:48:07: 11000000 INFO @ Wed, 08 Dec 2021 18:48:07: 16000000 INFO @ Wed, 08 Dec 2021 18:48:11: 17000000 INFO @ Wed, 08 Dec 2021 18:48:17: 17000000 INFO @ Wed, 08 Dec 2021 18:48:17: 12000000 INFO @ Wed, 08 Dec 2021 18:48:21: 18000000 INFO @ Wed, 08 Dec 2021 18:48:26: 18000000 INFO @ Wed, 08 Dec 2021 18:48:27: 13000000 INFO @ Wed, 08 Dec 2021 18:48:31: 19000000 INFO @ Wed, 08 Dec 2021 18:48:34: 19000000 INFO @ Wed, 08 Dec 2021 18:48:37: 14000000 INFO @ Wed, 08 Dec 2021 18:48:41: 20000000 INFO @ Wed, 08 Dec 2021 18:48:43: 20000000 INFO @ Wed, 08 Dec 2021 18:48:47: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:48:51: 21000000 INFO @ Wed, 08 Dec 2021 18:48:52: 21000000 INFO @ Wed, 08 Dec 2021 18:48:57: 16000000 INFO @ Wed, 08 Dec 2021 18:49:01: 22000000 INFO @ Wed, 08 Dec 2021 18:49:01: 22000000 INFO @ Wed, 08 Dec 2021 18:49:08: 17000000 INFO @ Wed, 08 Dec 2021 18:49:11: 23000000 INFO @ Wed, 08 Dec 2021 18:49:12: 23000000 INFO @ Wed, 08 Dec 2021 18:49:18: 18000000 INFO @ Wed, 08 Dec 2021 18:49:20: 24000000 INFO @ Wed, 08 Dec 2021 18:49:22: 24000000 INFO @ Wed, 08 Dec 2021 18:49:28: 19000000 INFO @ Wed, 08 Dec 2021 18:49:30: 25000000 INFO @ Wed, 08 Dec 2021 18:49:32: 25000000 INFO @ Wed, 08 Dec 2021 18:49:38: 20000000 INFO @ Wed, 08 Dec 2021 18:49:39: 26000000 INFO @ Wed, 08 Dec 2021 18:49:42: 26000000 INFO @ Wed, 08 Dec 2021 18:49:47: 21000000 INFO @ Wed, 08 Dec 2021 18:49:48: 27000000 INFO @ Wed, 08 Dec 2021 18:49:51: 27000000 INFO @ Wed, 08 Dec 2021 18:49:56: 28000000 INFO @ Wed, 08 Dec 2021 18:49:56: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:49:56: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:49:56: #1 total tags in treatment: 13873923 INFO @ Wed, 08 Dec 2021 18:49:56: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:49:56: #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 18:49:57: #1 tags after filtering in treatment: 12961183 INFO @ Wed, 08 Dec 2021 18:49:57: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 18:49:57: #1 finished! INFO @ Wed, 08 Dec 2021 18:49:57: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:49:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:49:57: 22000000 INFO @ Wed, 08 Dec 2021 18:49:58: #2 number of paired peaks: 321 WARNING @ Wed, 08 Dec 2021 18:49:58: 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 18:49:58: start model_add_line... INFO @ Wed, 08 Dec 2021 18:49:58: start X-correlation... INFO @ Wed, 08 Dec 2021 18:49:58: end of X-cor INFO @ Wed, 08 Dec 2021 18:49:58: #2 finished! INFO @ Wed, 08 Dec 2021 18:49:58: #2 predicted fragment length is 138 bps INFO @ Wed, 08 Dec 2021 18:49:58: #2 alternative fragment length(s) may be 4,138 bps INFO @ Wed, 08 Dec 2021 18:49:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976715/SRX8976715.10_model.r INFO @ Wed, 08 Dec 2021 18:49:58: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:49:58: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:50:01: 28000000 INFO @ Wed, 08 Dec 2021 18:50:01: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:50:01: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:50:01: #1 total tags in treatment: 13873923 INFO @ Wed, 08 Dec 2021 18:50:01: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:50:01: #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 18:50:01: #1 tags after filtering in treatment: 12961183 INFO @ Wed, 08 Dec 2021 18:50:01: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 18:50:01: #1 finished! INFO @ Wed, 08 Dec 2021 18:50:01: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:50:01: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:50:02: #2 number of paired peaks: 321 WARNING @ Wed, 08 Dec 2021 18:50:02: 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 18:50:02: start model_add_line... INFO @ Wed, 08 Dec 2021 18:50:02: start X-correlation... INFO @ Wed, 08 Dec 2021 18:50:02: end of X-cor INFO @ Wed, 08 Dec 2021 18:50:02: #2 finished! INFO @ Wed, 08 Dec 2021 18:50:02: #2 predicted fragment length is 138 bps INFO @ Wed, 08 Dec 2021 18:50:02: #2 alternative fragment length(s) may be 4,138 bps INFO @ Wed, 08 Dec 2021 18:50:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976715/SRX8976715.05_model.r INFO @ Wed, 08 Dec 2021 18:50:02: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:50:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:50:07: 23000000 INFO @ Wed, 08 Dec 2021 18:50:16: 24000000 INFO @ Wed, 08 Dec 2021 18:50:21: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:50:26: 25000000 INFO @ Wed, 08 Dec 2021 18:50:26: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:50:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976715/SRX8976715.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:50:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976715/SRX8976715.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:50:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976715/SRX8976715.10_summits.bed INFO @ Wed, 08 Dec 2021 18:50:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (270 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:50:35: 26000000 INFO @ Wed, 08 Dec 2021 18:50:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976715/SRX8976715.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:50:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976715/SRX8976715.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:50:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976715/SRX8976715.05_summits.bed INFO @ Wed, 08 Dec 2021 18:50:38: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (369 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:50:45: 27000000 INFO @ Wed, 08 Dec 2021 18:50:54: 28000000 INFO @ Wed, 08 Dec 2021 18:50:54: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:50:54: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:50:54: #1 total tags in treatment: 13873923 INFO @ Wed, 08 Dec 2021 18:50:54: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:50:54: #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 18:50:54: #1 tags after filtering in treatment: 12961183 INFO @ Wed, 08 Dec 2021 18:50:54: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 18:50:54: #1 finished! INFO @ Wed, 08 Dec 2021 18:50:54: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:50:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:50:55: #2 number of paired peaks: 321 WARNING @ Wed, 08 Dec 2021 18:50:55: 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 18:50:55: start model_add_line... INFO @ Wed, 08 Dec 2021 18:50:55: start X-correlation... INFO @ Wed, 08 Dec 2021 18:50:55: end of X-cor INFO @ Wed, 08 Dec 2021 18:50:55: #2 finished! INFO @ Wed, 08 Dec 2021 18:50:55: #2 predicted fragment length is 138 bps INFO @ Wed, 08 Dec 2021 18:50:55: #2 alternative fragment length(s) may be 4,138 bps INFO @ Wed, 08 Dec 2021 18:50:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976715/SRX8976715.20_model.r INFO @ Wed, 08 Dec 2021 18:50:55: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:50:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:51:19: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:51:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976715/SRX8976715.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:51:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976715/SRX8976715.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:51:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976715/SRX8976715.20_summits.bed INFO @ Wed, 08 Dec 2021 18:51:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (192 records, 4 fields): 1 millis CompletedMACS2peakCalling