Job ID = 14159055 SRX = SRX8976721 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14319811 spots for SRR12483325/SRR12483325.sra Written 14319811 spots for SRR12483325/SRR12483325.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159310 ("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: 00:12:30 14319811 reads; of these: 14319811 (100.00%) were paired; of these: 1367336 (9.55%) aligned concordantly 0 times 10697344 (74.70%) aligned concordantly exactly 1 time 2255131 (15.75%) aligned concordantly >1 times ---- 1367336 pairs aligned concordantly 0 times; of these: 780787 (57.10%) aligned discordantly 1 time ---- 586549 pairs aligned 0 times concordantly or discordantly; of these: 1173098 mates make up the pairs; of these: 690968 (58.90%) aligned 0 times 194574 (16.59%) aligned exactly 1 time 287556 (24.51%) aligned >1 times 97.59% overall alignment rate Time searching: 00:12:30 Overall time: 00:12:30 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] 5883144 / 13728261 = 0.4285 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 18:58:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976721/SRX8976721.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976721/SRX8976721.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976721/SRX8976721.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976721/SRX8976721.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 18:58:53: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:58:53: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:58:57: 1000000 INFO @ Wed, 08 Dec 2021 18:59:01: 2000000 INFO @ Wed, 08 Dec 2021 18:59:05: 3000000 INFO @ Wed, 08 Dec 2021 18:59:10: 4000000 INFO @ Wed, 08 Dec 2021 18:59:14: 5000000 INFO @ Wed, 08 Dec 2021 18:59:18: 6000000 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 18:59:22: 7000000 INFO @ Wed, 08 Dec 2021 18:59:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976721/SRX8976721.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976721/SRX8976721.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976721/SRX8976721.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976721/SRX8976721.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 18:59:23: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:59:23: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:59:26: 8000000 INFO @ Wed, 08 Dec 2021 18:59:27: 1000000 INFO @ Wed, 08 Dec 2021 18:59:31: 9000000 INFO @ Wed, 08 Dec 2021 18:59:32: 2000000 INFO @ Wed, 08 Dec 2021 18:59:35: 10000000 INFO @ Wed, 08 Dec 2021 18:59:36: 3000000 INFO @ Wed, 08 Dec 2021 18:59:39: 11000000 INFO @ Wed, 08 Dec 2021 18:59:40: 4000000 INFO @ Wed, 08 Dec 2021 18:59:43: 12000000 INFO @ Wed, 08 Dec 2021 18:59:45: 5000000 INFO @ Wed, 08 Dec 2021 18:59:48: 13000000 INFO @ Wed, 08 Dec 2021 18:59:49: 6000000 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 18:59:52: 14000000 INFO @ Wed, 08 Dec 2021 18:59:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976721/SRX8976721.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976721/SRX8976721.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976721/SRX8976721.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976721/SRX8976721.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 18:59:53: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:59:53: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:59:53: 7000000 INFO @ Wed, 08 Dec 2021 18:59:56: 15000000 INFO @ Wed, 08 Dec 2021 18:59:58: 8000000 INFO @ Wed, 08 Dec 2021 18:59:58: 1000000 INFO @ Wed, 08 Dec 2021 19:00:01: 16000000 INFO @ Wed, 08 Dec 2021 19:00:02: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 19:00:02: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 19:00:02: #1 total tags in treatment: 7301985 INFO @ Wed, 08 Dec 2021 19:00:02: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:00:02: #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 19:00:02: #1 tags after filtering in treatment: 6746036 INFO @ Wed, 08 Dec 2021 19:00:02: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 19:00:02: #1 finished! INFO @ Wed, 08 Dec 2021 19:00:02: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:00:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:00:02: 9000000 INFO @ Wed, 08 Dec 2021 19:00:02: #2 number of paired peaks: 881 WARNING @ Wed, 08 Dec 2021 19:00:02: Fewer paired peaks (881) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 881 pairs to build model! INFO @ Wed, 08 Dec 2021 19:00:02: start model_add_line... INFO @ Wed, 08 Dec 2021 19:00:02: start X-correlation... INFO @ Wed, 08 Dec 2021 19:00:02: end of X-cor INFO @ Wed, 08 Dec 2021 19:00:02: #2 finished! INFO @ Wed, 08 Dec 2021 19:00:02: #2 predicted fragment length is 178 bps INFO @ Wed, 08 Dec 2021 19:00:02: #2 alternative fragment length(s) may be 4,178 bps INFO @ Wed, 08 Dec 2021 19:00:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976721/SRX8976721.05_model.r INFO @ Wed, 08 Dec 2021 19:00:03: 2000000 INFO @ Wed, 08 Dec 2021 19:00:03: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:00:03: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:00:06: 10000000 INFO @ Wed, 08 Dec 2021 19:00:07: 3000000 INFO @ Wed, 08 Dec 2021 19:00:10: 11000000 INFO @ Wed, 08 Dec 2021 19:00:12: 4000000 INFO @ Wed, 08 Dec 2021 19:00:15: 12000000 INFO @ Wed, 08 Dec 2021 19:00:17: 5000000 INFO @ Wed, 08 Dec 2021 19:00:18: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:00:19: 13000000 INFO @ Wed, 08 Dec 2021 19:00:22: 6000000 INFO @ Wed, 08 Dec 2021 19:00:23: 14000000 INFO @ Wed, 08 Dec 2021 19:00:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976721/SRX8976721.05_peaks.xls INFO @ Wed, 08 Dec 2021 19:00:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976721/SRX8976721.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:00:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976721/SRX8976721.05_summits.bed INFO @ Wed, 08 Dec 2021 19:00:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (779 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 19:00:26: 7000000 INFO @ Wed, 08 Dec 2021 19:00:28: 15000000 INFO @ Wed, 08 Dec 2021 19:00:31: 8000000 INFO @ Wed, 08 Dec 2021 19:00:32: 16000000 INFO @ Wed, 08 Dec 2021 19:00:33: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 19:00:33: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 19:00:33: #1 total tags in treatment: 7301985 INFO @ Wed, 08 Dec 2021 19:00:33: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:00:33: #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 19:00:33: #1 tags after filtering in treatment: 6746036 INFO @ Wed, 08 Dec 2021 19:00:33: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 19:00:33: #1 finished! INFO @ Wed, 08 Dec 2021 19:00:33: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:00:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:00:33: #2 number of paired peaks: 881 WARNING @ Wed, 08 Dec 2021 19:00:33: Fewer paired peaks (881) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 881 pairs to build model! INFO @ Wed, 08 Dec 2021 19:00:33: start model_add_line... INFO @ Wed, 08 Dec 2021 19:00:33: start X-correlation... INFO @ Wed, 08 Dec 2021 19:00:33: end of X-cor INFO @ Wed, 08 Dec 2021 19:00:33: #2 finished! INFO @ Wed, 08 Dec 2021 19:00:33: #2 predicted fragment length is 178 bps INFO @ Wed, 08 Dec 2021 19:00:33: #2 alternative fragment length(s) may be 4,178 bps INFO @ Wed, 08 Dec 2021 19:00:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976721/SRX8976721.10_model.r INFO @ Wed, 08 Dec 2021 19:00:33: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:00:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:00:35: 9000000 INFO @ Wed, 08 Dec 2021 19:00:39: 10000000 INFO @ Wed, 08 Dec 2021 19:00:44: 11000000 INFO @ Wed, 08 Dec 2021 19:00:48: 12000000 INFO @ Wed, 08 Dec 2021 19:00:49: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:00:52: 13000000 INFO @ Wed, 08 Dec 2021 19:00:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976721/SRX8976721.10_peaks.xls INFO @ Wed, 08 Dec 2021 19:00:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976721/SRX8976721.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:00:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976721/SRX8976721.10_summits.bed INFO @ Wed, 08 Dec 2021 19:00:56: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (386 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 19:00:56: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 19:01:00: 15000000 INFO @ Wed, 08 Dec 2021 19:01:05: 16000000 INFO @ Wed, 08 Dec 2021 19:01:05: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 19:01:05: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 19:01:05: #1 total tags in treatment: 7301985 INFO @ Wed, 08 Dec 2021 19:01:05: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:01:05: #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 19:01:05: #1 tags after filtering in treatment: 6746036 INFO @ Wed, 08 Dec 2021 19:01:05: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 19:01:05: #1 finished! INFO @ Wed, 08 Dec 2021 19:01:05: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:01:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:01:06: #2 number of paired peaks: 881 WARNING @ Wed, 08 Dec 2021 19:01:06: Fewer paired peaks (881) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 881 pairs to build model! INFO @ Wed, 08 Dec 2021 19:01:06: start model_add_line... INFO @ Wed, 08 Dec 2021 19:01:06: start X-correlation... INFO @ Wed, 08 Dec 2021 19:01:06: end of X-cor INFO @ Wed, 08 Dec 2021 19:01:06: #2 finished! INFO @ Wed, 08 Dec 2021 19:01:06: #2 predicted fragment length is 178 bps INFO @ Wed, 08 Dec 2021 19:01:06: #2 alternative fragment length(s) may be 4,178 bps INFO @ Wed, 08 Dec 2021 19:01:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976721/SRX8976721.20_model.r INFO @ Wed, 08 Dec 2021 19:01:06: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:01:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:01:21: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 19:01:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976721/SRX8976721.20_peaks.xls INFO @ Wed, 08 Dec 2021 19:01:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976721/SRX8976721.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:01:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976721/SRX8976721.20_summits.bed INFO @ Wed, 08 Dec 2021 19:01:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (236 records, 4 fields): 1 millis CompletedMACS2peakCalling