Job ID = 14158263 SRX = SRX10342582 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7047734 spots for SRR13964620/SRR13964620.sra Written 7047734 spots for SRR13964620/SRR13964620.sra Read 7869655 spots for SRR13964621/SRR13964621.sra Written 7869655 spots for SRR13964621/SRR13964621.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158788 ("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: 00:10:13 14917389 reads; of these: 14917389 (100.00%) were paired; of these: 2364884 (15.85%) aligned concordantly 0 times 10881180 (72.94%) aligned concordantly exactly 1 time 1671325 (11.20%) aligned concordantly >1 times ---- 2364884 pairs aligned concordantly 0 times; of these: 1808402 (76.47%) aligned discordantly 1 time ---- 556482 pairs aligned 0 times concordantly or discordantly; of these: 1112964 mates make up the pairs; of these: 339656 (30.52%) aligned 0 times 312161 (28.05%) aligned exactly 1 time 461147 (41.43%) aligned >1 times 98.86% overall alignment rate Time searching: 00:10:13 Overall time: 00:10:13 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 8 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] 757414 / 14342821 = 0.0528 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 15:47:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342582/SRX10342582.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342582/SRX10342582.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342582/SRX10342582.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342582/SRX10342582.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 15:47:43: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:47:43: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:47:48: 1000000 INFO @ Wed, 08 Dec 2021 15:47:52: 2000000 INFO @ Wed, 08 Dec 2021 15:47:57: 3000000 INFO @ Wed, 08 Dec 2021 15:48:02: 4000000 INFO @ Wed, 08 Dec 2021 15:48:06: 5000000 INFO @ Wed, 08 Dec 2021 15:48:11: 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 15:48:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342582/SRX10342582.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342582/SRX10342582.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342582/SRX10342582.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342582/SRX10342582.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 15:48:13: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:48:13: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:48:15: 7000000 INFO @ Wed, 08 Dec 2021 15:48:17: 1000000 INFO @ Wed, 08 Dec 2021 15:48:20: 8000000 INFO @ Wed, 08 Dec 2021 15:48:21: 2000000 INFO @ Wed, 08 Dec 2021 15:48:25: 9000000 INFO @ Wed, 08 Dec 2021 15:48:25: 3000000 INFO @ Wed, 08 Dec 2021 15:48:29: 4000000 INFO @ Wed, 08 Dec 2021 15:48:29: 10000000 INFO @ Wed, 08 Dec 2021 15:48:33: 5000000 INFO @ Wed, 08 Dec 2021 15:48:34: 11000000 INFO @ Wed, 08 Dec 2021 15:48:37: 6000000 INFO @ Wed, 08 Dec 2021 15:48:38: 12000000 INFO @ Wed, 08 Dec 2021 15:48:41: 7000000 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 15:48:43: 13000000 INFO @ Wed, 08 Dec 2021 15:48:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342582/SRX10342582.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342582/SRX10342582.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342582/SRX10342582.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342582/SRX10342582.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 15:48:43: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:48:43: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:48:45: 8000000 INFO @ Wed, 08 Dec 2021 15:48:47: 1000000 INFO @ Wed, 08 Dec 2021 15:48:48: 14000000 INFO @ Wed, 08 Dec 2021 15:48:49: 9000000 INFO @ Wed, 08 Dec 2021 15:48:51: 2000000 INFO @ Wed, 08 Dec 2021 15:48:52: 15000000 INFO @ Wed, 08 Dec 2021 15:48:53: 10000000 INFO @ Wed, 08 Dec 2021 15:48:55: 3000000 INFO @ Wed, 08 Dec 2021 15:48:57: 11000000 INFO @ Wed, 08 Dec 2021 15:48:57: 16000000 INFO @ Wed, 08 Dec 2021 15:48:59: 4000000 INFO @ Wed, 08 Dec 2021 15:49:01: 12000000 INFO @ Wed, 08 Dec 2021 15:49:02: 17000000 INFO @ Wed, 08 Dec 2021 15:49:03: 5000000 INFO @ Wed, 08 Dec 2021 15:49:05: 13000000 INFO @ Wed, 08 Dec 2021 15:49:07: 18000000 INFO @ Wed, 08 Dec 2021 15:49:07: 6000000 INFO @ Wed, 08 Dec 2021 15:49:09: 14000000 INFO @ Wed, 08 Dec 2021 15:49:11: 7000000 INFO @ Wed, 08 Dec 2021 15:49:11: 19000000 INFO @ Wed, 08 Dec 2021 15:49:12: 15000000 INFO @ Wed, 08 Dec 2021 15:49:14: 8000000 INFO @ Wed, 08 Dec 2021 15:49:16: 20000000 INFO @ Wed, 08 Dec 2021 15:49:16: 16000000 INFO @ Wed, 08 Dec 2021 15:49:18: 9000000 INFO @ Wed, 08 Dec 2021 15:49:20: 17000000 INFO @ Wed, 08 Dec 2021 15:49:21: 21000000 INFO @ Wed, 08 Dec 2021 15:49:22: 10000000 INFO @ Wed, 08 Dec 2021 15:49:24: 18000000 INFO @ Wed, 08 Dec 2021 15:49:25: 22000000 INFO @ Wed, 08 Dec 2021 15:49:26: 11000000 INFO @ Wed, 08 Dec 2021 15:49:28: 19000000 INFO @ Wed, 08 Dec 2021 15:49:30: 23000000 INFO @ Wed, 08 Dec 2021 15:49:30: 12000000 INFO @ Wed, 08 Dec 2021 15:49:32: 20000000 INFO @ Wed, 08 Dec 2021 15:49:34: 13000000 INFO @ Wed, 08 Dec 2021 15:49:35: 24000000 INFO @ Wed, 08 Dec 2021 15:49:36: 21000000 INFO @ Wed, 08 Dec 2021 15:49:38: 14000000 INFO @ Wed, 08 Dec 2021 15:49:39: 25000000 INFO @ Wed, 08 Dec 2021 15:49:40: 22000000 INFO @ Wed, 08 Dec 2021 15:49:42: 15000000 INFO @ Wed, 08 Dec 2021 15:49:44: 26000000 INFO @ Wed, 08 Dec 2021 15:49:44: 23000000 INFO @ Wed, 08 Dec 2021 15:49:45: 16000000 INFO @ Wed, 08 Dec 2021 15:49:48: 24000000 INFO @ Wed, 08 Dec 2021 15:49:48: 27000000 INFO @ Wed, 08 Dec 2021 15:49:49: 17000000 INFO @ Wed, 08 Dec 2021 15:49:52: 25000000 INFO @ Wed, 08 Dec 2021 15:49:53: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 15:49:53: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 15:49:53: #1 total tags in treatment: 11869358 INFO @ Wed, 08 Dec 2021 15:49:53: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:49:53: #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 15:49:53: #1 tags after filtering in treatment: 10970267 INFO @ Wed, 08 Dec 2021 15:49:53: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 15:49:53: #1 finished! INFO @ Wed, 08 Dec 2021 15:49:53: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:49:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:49:53: 18000000 INFO @ Wed, 08 Dec 2021 15:49:54: #2 number of paired peaks: 387 WARNING @ Wed, 08 Dec 2021 15:49:54: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Wed, 08 Dec 2021 15:49:54: start model_add_line... INFO @ Wed, 08 Dec 2021 15:49:54: start X-correlation... INFO @ Wed, 08 Dec 2021 15:49:54: end of X-cor INFO @ Wed, 08 Dec 2021 15:49:54: #2 finished! INFO @ Wed, 08 Dec 2021 15:49:54: #2 predicted fragment length is 159 bps INFO @ Wed, 08 Dec 2021 15:49:54: #2 alternative fragment length(s) may be 4,115,159 bps INFO @ Wed, 08 Dec 2021 15:49:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342582/SRX10342582.05_model.r INFO @ Wed, 08 Dec 2021 15:49:54: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:49:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:49:55: 26000000 INFO @ Wed, 08 Dec 2021 15:49:57: 19000000 INFO @ Wed, 08 Dec 2021 15:49:59: 27000000 INFO @ Wed, 08 Dec 2021 15:50:01: 20000000 INFO @ Wed, 08 Dec 2021 15:50:03: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 15:50:03: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 15:50:03: #1 total tags in treatment: 11869358 INFO @ Wed, 08 Dec 2021 15:50:03: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:50:03: #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 15:50:03: #1 tags after filtering in treatment: 10970267 INFO @ Wed, 08 Dec 2021 15:50:03: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 15:50:03: #1 finished! INFO @ Wed, 08 Dec 2021 15:50:03: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:50:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:50:04: #2 number of paired peaks: 387 WARNING @ Wed, 08 Dec 2021 15:50:04: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Wed, 08 Dec 2021 15:50:04: start model_add_line... INFO @ Wed, 08 Dec 2021 15:50:04: start X-correlation... INFO @ Wed, 08 Dec 2021 15:50:04: end of X-cor INFO @ Wed, 08 Dec 2021 15:50:04: #2 finished! INFO @ Wed, 08 Dec 2021 15:50:04: #2 predicted fragment length is 159 bps INFO @ Wed, 08 Dec 2021 15:50:04: #2 alternative fragment length(s) may be 4,115,159 bps INFO @ Wed, 08 Dec 2021 15:50:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342582/SRX10342582.10_model.r INFO @ Wed, 08 Dec 2021 15:50:04: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:50:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:50:04: 21000000 INFO @ Wed, 08 Dec 2021 15:50:08: 22000000 INFO @ Wed, 08 Dec 2021 15:50:12: 23000000 INFO @ Wed, 08 Dec 2021 15:50:15: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:50:16: 24000000 INFO @ Wed, 08 Dec 2021 15:50:19: 25000000 INFO @ Wed, 08 Dec 2021 15:50:23: 26000000 INFO @ Wed, 08 Dec 2021 15:50:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342582/SRX10342582.05_peaks.xls INFO @ Wed, 08 Dec 2021 15:50:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342582/SRX10342582.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:50:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342582/SRX10342582.05_summits.bed INFO @ Wed, 08 Dec 2021 15:50:25: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (348 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 15:50:25: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:50:27: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 15:50:31: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 15:50:31: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 15:50:31: #1 total tags in treatment: 11869358 INFO @ Wed, 08 Dec 2021 15:50:31: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:50:31: #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 15:50:31: #1 tags after filtering in treatment: 10970267 INFO @ Wed, 08 Dec 2021 15:50:31: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 15:50:31: #1 finished! INFO @ Wed, 08 Dec 2021 15:50:31: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:50:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:50:31: #2 number of paired peaks: 387 WARNING @ Wed, 08 Dec 2021 15:50:31: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Wed, 08 Dec 2021 15:50:31: start model_add_line... INFO @ Wed, 08 Dec 2021 15:50:32: start X-correlation... INFO @ Wed, 08 Dec 2021 15:50:32: end of X-cor INFO @ Wed, 08 Dec 2021 15:50:32: #2 finished! INFO @ Wed, 08 Dec 2021 15:50:32: #2 predicted fragment length is 159 bps INFO @ Wed, 08 Dec 2021 15:50:32: #2 alternative fragment length(s) may be 4,115,159 bps INFO @ Wed, 08 Dec 2021 15:50:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342582/SRX10342582.20_model.r INFO @ Wed, 08 Dec 2021 15:50:32: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:50:32: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:50:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342582/SRX10342582.10_peaks.xls INFO @ Wed, 08 Dec 2021 15:50:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342582/SRX10342582.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:50:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342582/SRX10342582.10_summits.bed INFO @ Wed, 08 Dec 2021 15:50:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (261 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 15:50:52: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:51:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342582/SRX10342582.20_peaks.xls INFO @ Wed, 08 Dec 2021 15:51:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342582/SRX10342582.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:51:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342582/SRX10342582.20_summits.bed INFO @ Wed, 08 Dec 2021 15:51:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (180 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。