Job ID = 14158261 SRX = SRX10342580 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10533898 spots for SRR13964616/SRR13964616.sra Written 10533898 spots for SRR13964616/SRR13964616.sra Read 11542427 spots for SRR13964617/SRR13964617.sra Written 11542427 spots for SRR13964617/SRR13964617.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158801 ("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: 00:16:30 22076325 reads; of these: 22076325 (100.00%) were paired; of these: 8246750 (37.36%) aligned concordantly 0 times 11533174 (52.24%) aligned concordantly exactly 1 time 2296401 (10.40%) aligned concordantly >1 times ---- 8246750 pairs aligned concordantly 0 times; of these: 6059165 (73.47%) aligned discordantly 1 time ---- 2187585 pairs aligned 0 times concordantly or discordantly; of these: 4375170 mates make up the pairs; of these: 1948207 (44.53%) aligned 0 times 935812 (21.39%) aligned exactly 1 time 1491151 (34.08%) aligned >1 times 95.59% overall alignment rate Time searching: 00:16:30 Overall time: 00:16:30 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] 3756412 / 19878262 = 0.1890 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 15:55:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342580/SRX10342580.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342580/SRX10342580.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342580/SRX10342580.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342580/SRX10342580.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 15:55:36: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:55:36: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:55:40: 1000000 INFO @ Wed, 08 Dec 2021 15:55:44: 2000000 INFO @ Wed, 08 Dec 2021 15:55:48: 3000000 INFO @ Wed, 08 Dec 2021 15:55:52: 4000000 INFO @ Wed, 08 Dec 2021 15:55:56: 5000000 INFO @ Wed, 08 Dec 2021 15:56:00: 6000000 INFO @ Wed, 08 Dec 2021 15:56:04: 7000000 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 15:56:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342580/SRX10342580.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342580/SRX10342580.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342580/SRX10342580.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342580/SRX10342580.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 15:56:06: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:56:06: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:56:08: 8000000 INFO @ Wed, 08 Dec 2021 15:56:10: 1000000 INFO @ Wed, 08 Dec 2021 15:56:12: 9000000 INFO @ Wed, 08 Dec 2021 15:56:14: 2000000 INFO @ Wed, 08 Dec 2021 15:56:16: 10000000 INFO @ Wed, 08 Dec 2021 15:56:18: 3000000 INFO @ Wed, 08 Dec 2021 15:56:20: 11000000 INFO @ Wed, 08 Dec 2021 15:56:23: 4000000 INFO @ Wed, 08 Dec 2021 15:56:24: 12000000 INFO @ Wed, 08 Dec 2021 15:56:27: 5000000 INFO @ Wed, 08 Dec 2021 15:56:28: 13000000 INFO @ Wed, 08 Dec 2021 15:56:31: 6000000 INFO @ Wed, 08 Dec 2021 15:56:32: 14000000 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 15:56:35: 7000000 INFO @ Wed, 08 Dec 2021 15:56:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342580/SRX10342580.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342580/SRX10342580.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342580/SRX10342580.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342580/SRX10342580.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 15:56:36: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:56:36: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:56:36: 15000000 INFO @ Wed, 08 Dec 2021 15:56:39: 8000000 INFO @ Wed, 08 Dec 2021 15:56:40: 1000000 INFO @ Wed, 08 Dec 2021 15:56:41: 16000000 INFO @ Wed, 08 Dec 2021 15:56:43: 9000000 INFO @ Wed, 08 Dec 2021 15:56:44: 2000000 INFO @ Wed, 08 Dec 2021 15:56:45: 17000000 INFO @ Wed, 08 Dec 2021 15:56:47: 10000000 INFO @ Wed, 08 Dec 2021 15:56:49: 3000000 INFO @ Wed, 08 Dec 2021 15:56:49: 18000000 INFO @ Wed, 08 Dec 2021 15:56:51: 11000000 INFO @ Wed, 08 Dec 2021 15:56:53: 4000000 INFO @ Wed, 08 Dec 2021 15:56:53: 19000000 INFO @ Wed, 08 Dec 2021 15:56:56: 12000000 INFO @ Wed, 08 Dec 2021 15:56:57: 5000000 INFO @ Wed, 08 Dec 2021 15:56:57: 20000000 INFO @ Wed, 08 Dec 2021 15:57:00: 13000000 INFO @ Wed, 08 Dec 2021 15:57:01: 6000000 INFO @ Wed, 08 Dec 2021 15:57:01: 21000000 INFO @ Wed, 08 Dec 2021 15:57:04: 14000000 INFO @ Wed, 08 Dec 2021 15:57:05: 7000000 INFO @ Wed, 08 Dec 2021 15:57:05: 22000000 INFO @ Wed, 08 Dec 2021 15:57:08: 15000000 INFO @ Wed, 08 Dec 2021 15:57:09: 8000000 INFO @ Wed, 08 Dec 2021 15:57:10: 23000000 INFO @ Wed, 08 Dec 2021 15:57:12: 16000000 INFO @ Wed, 08 Dec 2021 15:57:13: 9000000 INFO @ Wed, 08 Dec 2021 15:57:14: 24000000 INFO @ Wed, 08 Dec 2021 15:57:16: 17000000 INFO @ Wed, 08 Dec 2021 15:57:17: 10000000 INFO @ Wed, 08 Dec 2021 15:57:18: 25000000 INFO @ Wed, 08 Dec 2021 15:57:20: 18000000 INFO @ Wed, 08 Dec 2021 15:57:21: 11000000 INFO @ Wed, 08 Dec 2021 15:57:22: 26000000 INFO @ Wed, 08 Dec 2021 15:57:24: 19000000 INFO @ Wed, 08 Dec 2021 15:57:25: 12000000 INFO @ Wed, 08 Dec 2021 15:57:26: 27000000 INFO @ Wed, 08 Dec 2021 15:57:29: 20000000 INFO @ Wed, 08 Dec 2021 15:57:30: 13000000 INFO @ Wed, 08 Dec 2021 15:57:30: 28000000 INFO @ Wed, 08 Dec 2021 15:57:33: 21000000 INFO @ Wed, 08 Dec 2021 15:57:34: 14000000 INFO @ Wed, 08 Dec 2021 15:57:34: 29000000 INFO @ Wed, 08 Dec 2021 15:57:37: 22000000 INFO @ Wed, 08 Dec 2021 15:57:38: 15000000 INFO @ Wed, 08 Dec 2021 15:57:38: 30000000 INFO @ Wed, 08 Dec 2021 15:57:41: 23000000 INFO @ Wed, 08 Dec 2021 15:57:42: 16000000 INFO @ Wed, 08 Dec 2021 15:57:42: 31000000 INFO @ Wed, 08 Dec 2021 15:57:45: 24000000 INFO @ Wed, 08 Dec 2021 15:57:46: 17000000 INFO @ Wed, 08 Dec 2021 15:57:46: 32000000 INFO @ Wed, 08 Dec 2021 15:57:49: 25000000 INFO @ Wed, 08 Dec 2021 15:57:50: 18000000 INFO @ Wed, 08 Dec 2021 15:57:50: 33000000 INFO @ Wed, 08 Dec 2021 15:57:53: 26000000 INFO @ Wed, 08 Dec 2021 15:57:54: 19000000 INFO @ Wed, 08 Dec 2021 15:57:54: 34000000 INFO @ Wed, 08 Dec 2021 15:57:57: 27000000 INFO @ Wed, 08 Dec 2021 15:57:57: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 15:57:57: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 15:57:57: #1 total tags in treatment: 11019619 INFO @ Wed, 08 Dec 2021 15:57:57: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:57:57: #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 15:57:58: #1 tags after filtering in treatment: 9965077 INFO @ Wed, 08 Dec 2021 15:57:58: #1 Redundant rate of treatment: 0.10 INFO @ Wed, 08 Dec 2021 15:57:58: #1 finished! INFO @ Wed, 08 Dec 2021 15:57:58: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:57:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:57:58: 20000000 INFO @ Wed, 08 Dec 2021 15:57:58: #2 number of paired peaks: 615 WARNING @ Wed, 08 Dec 2021 15:57:58: Fewer paired peaks (615) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 615 pairs to build model! INFO @ Wed, 08 Dec 2021 15:57:58: start model_add_line... INFO @ Wed, 08 Dec 2021 15:57:58: start X-correlation... INFO @ Wed, 08 Dec 2021 15:57:58: end of X-cor INFO @ Wed, 08 Dec 2021 15:57:58: #2 finished! INFO @ Wed, 08 Dec 2021 15:57:58: #2 predicted fragment length is 136 bps INFO @ Wed, 08 Dec 2021 15:57:58: #2 alternative fragment length(s) may be 4,112,136 bps INFO @ Wed, 08 Dec 2021 15:57:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342580/SRX10342580.05_model.r INFO @ Wed, 08 Dec 2021 15:57:58: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:57:58: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:58:01: 28000000 INFO @ Wed, 08 Dec 2021 15:58:02: 21000000 INFO @ Wed, 08 Dec 2021 15:58:05: 29000000 INFO @ Wed, 08 Dec 2021 15:58:06: 22000000 INFO @ Wed, 08 Dec 2021 15:58:09: 30000000 INFO @ Wed, 08 Dec 2021 15:58:10: 23000000 INFO @ Wed, 08 Dec 2021 15:58:13: 31000000 INFO @ Wed, 08 Dec 2021 15:58:14: 24000000 INFO @ Wed, 08 Dec 2021 15:58:17: 32000000 INFO @ Wed, 08 Dec 2021 15:58:18: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:58:18: 25000000 INFO @ Wed, 08 Dec 2021 15:58:21: 33000000 INFO @ Wed, 08 Dec 2021 15:58:22: 26000000 INFO @ Wed, 08 Dec 2021 15:58:25: 34000000 INFO @ Wed, 08 Dec 2021 15:58:26: 27000000 INFO @ Wed, 08 Dec 2021 15:58:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342580/SRX10342580.05_peaks.xls INFO @ Wed, 08 Dec 2021 15:58:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342580/SRX10342580.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:58:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342580/SRX10342580.05_summits.bed INFO @ Wed, 08 Dec 2021 15:58:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (490 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 15:58:28: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 15:58:28: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 15:58:28: #1 total tags in treatment: 11019619 INFO @ Wed, 08 Dec 2021 15:58:28: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:58:28: #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 15:58:28: #1 tags after filtering in treatment: 9965077 INFO @ Wed, 08 Dec 2021 15:58:28: #1 Redundant rate of treatment: 0.10 INFO @ Wed, 08 Dec 2021 15:58:28: #1 finished! INFO @ Wed, 08 Dec 2021 15:58:28: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:58:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:58:29: #2 number of paired peaks: 615 WARNING @ Wed, 08 Dec 2021 15:58:29: Fewer paired peaks (615) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 615 pairs to build model! INFO @ Wed, 08 Dec 2021 15:58:29: start model_add_line... INFO @ Wed, 08 Dec 2021 15:58:29: start X-correlation... INFO @ Wed, 08 Dec 2021 15:58:29: end of X-cor INFO @ Wed, 08 Dec 2021 15:58:29: #2 finished! INFO @ Wed, 08 Dec 2021 15:58:29: #2 predicted fragment length is 136 bps INFO @ Wed, 08 Dec 2021 15:58:29: #2 alternative fragment length(s) may be 4,112,136 bps INFO @ Wed, 08 Dec 2021 15:58:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342580/SRX10342580.10_model.r INFO @ Wed, 08 Dec 2021 15:58:29: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:58:29: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:58:30: 28000000 INFO @ Wed, 08 Dec 2021 15:58:34: 29000000 INFO @ Wed, 08 Dec 2021 15:58:38: 30000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 15:58:42: 31000000 INFO @ Wed, 08 Dec 2021 15:58:46: 32000000 INFO @ Wed, 08 Dec 2021 15:58:49: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:58:50: 33000000 INFO @ Wed, 08 Dec 2021 15:58:54: 34000000 INFO @ Wed, 08 Dec 2021 15:58:56: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 15:58:56: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 15:58:56: #1 total tags in treatment: 11019619 INFO @ Wed, 08 Dec 2021 15:58:56: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:58:56: #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 15:58:57: #1 tags after filtering in treatment: 9965077 INFO @ Wed, 08 Dec 2021 15:58:57: #1 Redundant rate of treatment: 0.10 INFO @ Wed, 08 Dec 2021 15:58:57: #1 finished! INFO @ Wed, 08 Dec 2021 15:58:57: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:58:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:58:57: #2 number of paired peaks: 615 WARNING @ Wed, 08 Dec 2021 15:58:57: Fewer paired peaks (615) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 615 pairs to build model! INFO @ Wed, 08 Dec 2021 15:58:57: start model_add_line... INFO @ Wed, 08 Dec 2021 15:58:57: start X-correlation... INFO @ Wed, 08 Dec 2021 15:58:57: end of X-cor INFO @ Wed, 08 Dec 2021 15:58:57: #2 finished! INFO @ Wed, 08 Dec 2021 15:58:57: #2 predicted fragment length is 136 bps INFO @ Wed, 08 Dec 2021 15:58:57: #2 alternative fragment length(s) may be 4,112,136 bps INFO @ Wed, 08 Dec 2021 15:58:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342580/SRX10342580.20_model.r INFO @ Wed, 08 Dec 2021 15:58:57: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:58:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:58:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342580/SRX10342580.10_peaks.xls INFO @ Wed, 08 Dec 2021 15:58:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342580/SRX10342580.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:58:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342580/SRX10342580.10_summits.bed INFO @ Wed, 08 Dec 2021 15:58:59: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (360 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 15:59:17: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:59:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342580/SRX10342580.20_peaks.xls INFO @ Wed, 08 Dec 2021 15:59:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342580/SRX10342580.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:59:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342580/SRX10342580.20_summits.bed INFO @ Wed, 08 Dec 2021 15:59:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (250 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。