Job ID = 14158335 SRX = SRX10342597 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9849568 spots for SRR13964650/SRR13964650.sra Written 9849568 spots for SRR13964650/SRR13964650.sra Read 10973896 spots for SRR13964651/SRR13964651.sra Written 10973896 spots for SRR13964651/SRR13964651.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158930 ("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: 00:18:36 20823464 reads; of these: 20823464 (100.00%) were paired; of these: 3536356 (16.98%) aligned concordantly 0 times 15324567 (73.59%) aligned concordantly exactly 1 time 1962541 (9.42%) aligned concordantly >1 times ---- 3536356 pairs aligned concordantly 0 times; of these: 2416229 (68.33%) aligned discordantly 1 time ---- 1120127 pairs aligned 0 times concordantly or discordantly; of these: 2240254 mates make up the pairs; of these: 1269871 (56.68%) aligned 0 times 405818 (18.11%) aligned exactly 1 time 564565 (25.20%) aligned >1 times 96.95% overall alignment rate Time searching: 00:18:36 Overall time: 00:18:36 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] 2880022 / 19689687 = 0.1463 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 16:45:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342597/SRX10342597.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342597/SRX10342597.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342597/SRX10342597.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342597/SRX10342597.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 16:45:13: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:45:13: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:45:21: 1000000 INFO @ Wed, 08 Dec 2021 16:45:29: 2000000 INFO @ Wed, 08 Dec 2021 16:45:36: 3000000 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 16:45:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342597/SRX10342597.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342597/SRX10342597.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342597/SRX10342597.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342597/SRX10342597.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 16:45:42: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:45:42: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:45:44: 4000000 INFO @ Wed, 08 Dec 2021 16:45:49: 1000000 INFO @ Wed, 08 Dec 2021 16:45:53: 5000000 INFO @ Wed, 08 Dec 2021 16:45:56: 2000000 INFO @ Wed, 08 Dec 2021 16:46:03: 6000000 INFO @ Wed, 08 Dec 2021 16:46:03: 3000000 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 16:46:10: 4000000 INFO @ Wed, 08 Dec 2021 16:46:12: 7000000 INFO @ Wed, 08 Dec 2021 16:46:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342597/SRX10342597.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342597/SRX10342597.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342597/SRX10342597.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342597/SRX10342597.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 16:46:12: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:46:12: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:46:19: 5000000 INFO @ Wed, 08 Dec 2021 16:46:20: 1000000 INFO @ Wed, 08 Dec 2021 16:46:22: 8000000 INFO @ Wed, 08 Dec 2021 16:46:28: 6000000 INFO @ Wed, 08 Dec 2021 16:46:28: 2000000 INFO @ Wed, 08 Dec 2021 16:46:31: 9000000 INFO @ Wed, 08 Dec 2021 16:46:36: 3000000 INFO @ Wed, 08 Dec 2021 16:46:37: 7000000 INFO @ Wed, 08 Dec 2021 16:46:40: 10000000 INFO @ Wed, 08 Dec 2021 16:46:45: 4000000 INFO @ Wed, 08 Dec 2021 16:46:45: 8000000 INFO @ Wed, 08 Dec 2021 16:46:49: 11000000 INFO @ Wed, 08 Dec 2021 16:46:54: 9000000 INFO @ Wed, 08 Dec 2021 16:46:55: 5000000 INFO @ Wed, 08 Dec 2021 16:47:00: 12000000 INFO @ Wed, 08 Dec 2021 16:47:01: 10000000 INFO @ Wed, 08 Dec 2021 16:47:06: 6000000 INFO @ Wed, 08 Dec 2021 16:47:10: 11000000 INFO @ Wed, 08 Dec 2021 16:47:10: 13000000 INFO @ Wed, 08 Dec 2021 16:47:16: 7000000 INFO @ Wed, 08 Dec 2021 16:47:18: 12000000 INFO @ Wed, 08 Dec 2021 16:47:20: 14000000 INFO @ Wed, 08 Dec 2021 16:47:26: 8000000 INFO @ Wed, 08 Dec 2021 16:47:27: 13000000 INFO @ Wed, 08 Dec 2021 16:47:31: 15000000 INFO @ Wed, 08 Dec 2021 16:47:36: 9000000 INFO @ Wed, 08 Dec 2021 16:47:36: 14000000 INFO @ Wed, 08 Dec 2021 16:47:41: 16000000 INFO @ Wed, 08 Dec 2021 16:47:44: 10000000 INFO @ Wed, 08 Dec 2021 16:47:45: 15000000 INFO @ Wed, 08 Dec 2021 16:47:51: 17000000 INFO @ Wed, 08 Dec 2021 16:47:54: 16000000 INFO @ Wed, 08 Dec 2021 16:47:54: 11000000 INFO @ Wed, 08 Dec 2021 16:48:02: 18000000 INFO @ Wed, 08 Dec 2021 16:48:03: 17000000 INFO @ Wed, 08 Dec 2021 16:48:05: 12000000 INFO @ Wed, 08 Dec 2021 16:48:12: 18000000 INFO @ Wed, 08 Dec 2021 16:48:12: 19000000 INFO @ Wed, 08 Dec 2021 16:48:16: 13000000 INFO @ Wed, 08 Dec 2021 16:48:21: 19000000 INFO @ Wed, 08 Dec 2021 16:48:23: 20000000 INFO @ Wed, 08 Dec 2021 16:48:26: 14000000 INFO @ Wed, 08 Dec 2021 16:48:30: 20000000 INFO @ Wed, 08 Dec 2021 16:48:33: 21000000 INFO @ Wed, 08 Dec 2021 16:48:37: 15000000 INFO @ Wed, 08 Dec 2021 16:48:40: 21000000 INFO @ Wed, 08 Dec 2021 16:48:43: 22000000 INFO @ Wed, 08 Dec 2021 16:48:48: 16000000 INFO @ Wed, 08 Dec 2021 16:48:49: 22000000 INFO @ Wed, 08 Dec 2021 16:48:53: 23000000 INFO @ Wed, 08 Dec 2021 16:48:58: 23000000 INFO @ Wed, 08 Dec 2021 16:48:58: 17000000 INFO @ Wed, 08 Dec 2021 16:49:03: 24000000 INFO @ Wed, 08 Dec 2021 16:49:07: 24000000 INFO @ Wed, 08 Dec 2021 16:49:09: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 16:49:13: 25000000 INFO @ Wed, 08 Dec 2021 16:49:15: 25000000 INFO @ Wed, 08 Dec 2021 16:49:20: 19000000 INFO @ Wed, 08 Dec 2021 16:49:23: 26000000 INFO @ Wed, 08 Dec 2021 16:49:24: 26000000 INFO @ Wed, 08 Dec 2021 16:49:31: 20000000 INFO @ Wed, 08 Dec 2021 16:49:33: 27000000 INFO @ Wed, 08 Dec 2021 16:49:34: 27000000 INFO @ Wed, 08 Dec 2021 16:49:41: 21000000 INFO @ Wed, 08 Dec 2021 16:49:43: 28000000 INFO @ Wed, 08 Dec 2021 16:49:44: 28000000 INFO @ Wed, 08 Dec 2021 16:49:51: 22000000 INFO @ Wed, 08 Dec 2021 16:49:52: 29000000 INFO @ Wed, 08 Dec 2021 16:49:54: 29000000 INFO @ Wed, 08 Dec 2021 16:50:01: 23000000 INFO @ Wed, 08 Dec 2021 16:50:01: 30000000 INFO @ Wed, 08 Dec 2021 16:50:04: 30000000 INFO @ Wed, 08 Dec 2021 16:50:10: 31000000 INFO @ Wed, 08 Dec 2021 16:50:11: 24000000 INFO @ Wed, 08 Dec 2021 16:50:14: 31000000 INFO @ Wed, 08 Dec 2021 16:50:20: 32000000 INFO @ Wed, 08 Dec 2021 16:50:22: 25000000 INFO @ Wed, 08 Dec 2021 16:50:24: 32000000 INFO @ Wed, 08 Dec 2021 16:50:29: 33000000 INFO @ Wed, 08 Dec 2021 16:50:32: 26000000 INFO @ Wed, 08 Dec 2021 16:50:35: 33000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 16:50:38: 34000000 INFO @ Wed, 08 Dec 2021 16:50:42: 27000000 INFO @ Wed, 08 Dec 2021 16:50:43: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 16:50:43: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 16:50:43: #1 total tags in treatment: 14684016 INFO @ Wed, 08 Dec 2021 16:50:43: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:50:43: #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 16:50:44: #1 tags after filtering in treatment: 13504127 INFO @ Wed, 08 Dec 2021 16:50:44: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 16:50:44: #1 finished! INFO @ Wed, 08 Dec 2021 16:50:44: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:50:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:50:45: 34000000 INFO @ Wed, 08 Dec 2021 16:50:45: #2 number of paired peaks: 320 WARNING @ Wed, 08 Dec 2021 16:50:45: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Wed, 08 Dec 2021 16:50:45: start model_add_line... INFO @ Wed, 08 Dec 2021 16:50:45: start X-correlation... INFO @ Wed, 08 Dec 2021 16:50:45: end of X-cor INFO @ Wed, 08 Dec 2021 16:50:45: #2 finished! INFO @ Wed, 08 Dec 2021 16:50:45: #2 predicted fragment length is 166 bps INFO @ Wed, 08 Dec 2021 16:50:45: #2 alternative fragment length(s) may be 4,166 bps INFO @ Wed, 08 Dec 2021 16:50:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342597/SRX10342597.10_model.r INFO @ Wed, 08 Dec 2021 16:50:45: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:50:45: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:50:51: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 16:50:51: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 16:50:51: #1 total tags in treatment: 14684016 INFO @ Wed, 08 Dec 2021 16:50:51: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:50:51: #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 16:50:51: #1 tags after filtering in treatment: 13504127 INFO @ Wed, 08 Dec 2021 16:50:51: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 16:50:51: #1 finished! INFO @ Wed, 08 Dec 2021 16:50:51: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:50:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:50:52: 28000000 INFO @ Wed, 08 Dec 2021 16:50:52: #2 number of paired peaks: 320 WARNING @ Wed, 08 Dec 2021 16:50:52: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Wed, 08 Dec 2021 16:50:52: start model_add_line... INFO @ Wed, 08 Dec 2021 16:50:52: start X-correlation... INFO @ Wed, 08 Dec 2021 16:50:52: end of X-cor INFO @ Wed, 08 Dec 2021 16:50:52: #2 finished! INFO @ Wed, 08 Dec 2021 16:50:52: #2 predicted fragment length is 166 bps INFO @ Wed, 08 Dec 2021 16:50:52: #2 alternative fragment length(s) may be 4,166 bps INFO @ Wed, 08 Dec 2021 16:50:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342597/SRX10342597.05_model.r INFO @ Wed, 08 Dec 2021 16:50:53: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:50:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:51:01: 29000000 INFO @ Wed, 08 Dec 2021 16:51:10: 30000000 INFO @ Wed, 08 Dec 2021 16:51:19: 31000000 INFO @ Wed, 08 Dec 2021 16:51:24: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:51:27: 32000000 INFO @ Wed, 08 Dec 2021 16:51:32: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:51:37: 33000000 INFO @ Wed, 08 Dec 2021 16:51:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342597/SRX10342597.10_peaks.xls INFO @ Wed, 08 Dec 2021 16:51:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342597/SRX10342597.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:51:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342597/SRX10342597.10_summits.bed INFO @ Wed, 08 Dec 2021 16:51:45: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2103 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 16:51:46: 34000000 INFO @ Wed, 08 Dec 2021 16:51:51: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 16:51:51: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 16:51:51: #1 total tags in treatment: 14684016 INFO @ Wed, 08 Dec 2021 16:51:51: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:51:51: #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 16:51:51: #1 tags after filtering in treatment: 13504127 INFO @ Wed, 08 Dec 2021 16:51:51: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 16:51:51: #1 finished! INFO @ Wed, 08 Dec 2021 16:51:51: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:51:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:51:52: #2 number of paired peaks: 320 WARNING @ Wed, 08 Dec 2021 16:51:52: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Wed, 08 Dec 2021 16:51:52: start model_add_line... INFO @ Wed, 08 Dec 2021 16:51:53: start X-correlation... INFO @ Wed, 08 Dec 2021 16:51:53: end of X-cor INFO @ Wed, 08 Dec 2021 16:51:53: #2 finished! INFO @ Wed, 08 Dec 2021 16:51:53: #2 predicted fragment length is 166 bps INFO @ Wed, 08 Dec 2021 16:51:53: #2 alternative fragment length(s) may be 4,166 bps INFO @ Wed, 08 Dec 2021 16:51:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342597/SRX10342597.20_model.r INFO @ Wed, 08 Dec 2021 16:51:53: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:51:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:51:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342597/SRX10342597.05_peaks.xls INFO @ Wed, 08 Dec 2021 16:51:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342597/SRX10342597.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:51:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342597/SRX10342597.05_summits.bed INFO @ Wed, 08 Dec 2021 16:51:53: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (4462 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 16:52:31: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:52:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342597/SRX10342597.20_peaks.xls INFO @ Wed, 08 Dec 2021 16:52:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342597/SRX10342597.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:52:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342597/SRX10342597.20_summits.bed INFO @ Wed, 08 Dec 2021 16:52:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (479 records, 4 fields): 4 millis CompletedMACS2peakCalling