Job ID = 14158314 SRX = SRX10342590 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8573946 spots for SRR13964636/SRR13964636.sra Written 8573946 spots for SRR13964636/SRR13964636.sra Read 9404137 spots for SRR13964637/SRR13964637.sra Written 9404137 spots for SRR13964637/SRR13964637.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158871 ("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: 00:16:17 17978083 reads; of these: 17978083 (100.00%) were paired; of these: 5975336 (33.24%) aligned concordantly 0 times 10561184 (58.74%) aligned concordantly exactly 1 time 1441563 (8.02%) aligned concordantly >1 times ---- 5975336 pairs aligned concordantly 0 times; of these: 4511883 (75.51%) aligned discordantly 1 time ---- 1463453 pairs aligned 0 times concordantly or discordantly; of these: 2926906 mates make up the pairs; of these: 1293618 (44.20%) aligned 0 times 666080 (22.76%) aligned exactly 1 time 967208 (33.05%) aligned >1 times 96.40% overall alignment rate Time searching: 00:16:17 Overall time: 00:16:17 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] 2077169 / 16505578 = 0.1258 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 16:26:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342590/SRX10342590.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342590/SRX10342590.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342590/SRX10342590.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342590/SRX10342590.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 16:26:10: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:26:10: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:26:17: 1000000 INFO @ Wed, 08 Dec 2021 16:26:22: 2000000 INFO @ Wed, 08 Dec 2021 16:26:28: 3000000 INFO @ Wed, 08 Dec 2021 16:26:34: 4000000 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 16:26:40: 5000000 INFO @ Wed, 08 Dec 2021 16:26:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342590/SRX10342590.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342590/SRX10342590.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342590/SRX10342590.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342590/SRX10342590.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 16:26:40: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:26:40: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:26:46: 6000000 INFO @ Wed, 08 Dec 2021 16:26:47: 1000000 INFO @ Wed, 08 Dec 2021 16:26:52: 7000000 INFO @ Wed, 08 Dec 2021 16:26:54: 2000000 INFO @ Wed, 08 Dec 2021 16:26:58: 8000000 INFO @ Wed, 08 Dec 2021 16:27:00: 3000000 INFO @ Wed, 08 Dec 2021 16:27:03: 9000000 INFO @ Wed, 08 Dec 2021 16:27:07: 4000000 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 16:27:10: 10000000 INFO @ Wed, 08 Dec 2021 16:27:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342590/SRX10342590.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342590/SRX10342590.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342590/SRX10342590.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342590/SRX10342590.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 16:27:10: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:27:10: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:27:13: 5000000 INFO @ Wed, 08 Dec 2021 16:27:16: 11000000 INFO @ Wed, 08 Dec 2021 16:27:17: 1000000 INFO @ Wed, 08 Dec 2021 16:27:20: 6000000 INFO @ Wed, 08 Dec 2021 16:27:22: 12000000 INFO @ Wed, 08 Dec 2021 16:27:23: 2000000 INFO @ Wed, 08 Dec 2021 16:27:27: 7000000 INFO @ Wed, 08 Dec 2021 16:27:28: 13000000 INFO @ Wed, 08 Dec 2021 16:27:30: 3000000 INFO @ Wed, 08 Dec 2021 16:27:33: 8000000 INFO @ Wed, 08 Dec 2021 16:27:35: 14000000 INFO @ Wed, 08 Dec 2021 16:27:36: 4000000 INFO @ Wed, 08 Dec 2021 16:27:40: 9000000 INFO @ Wed, 08 Dec 2021 16:27:42: 15000000 INFO @ Wed, 08 Dec 2021 16:27:43: 5000000 INFO @ Wed, 08 Dec 2021 16:27:47: 10000000 INFO @ Wed, 08 Dec 2021 16:27:48: 16000000 INFO @ Wed, 08 Dec 2021 16:27:50: 6000000 INFO @ Wed, 08 Dec 2021 16:27:53: 11000000 INFO @ Wed, 08 Dec 2021 16:27:55: 17000000 INFO @ Wed, 08 Dec 2021 16:27:57: 7000000 INFO @ Wed, 08 Dec 2021 16:28:00: 12000000 INFO @ Wed, 08 Dec 2021 16:28:00: 18000000 INFO @ Wed, 08 Dec 2021 16:28:03: 8000000 INFO @ Wed, 08 Dec 2021 16:28:06: 19000000 INFO @ Wed, 08 Dec 2021 16:28:06: 13000000 INFO @ Wed, 08 Dec 2021 16:28:09: 9000000 INFO @ Wed, 08 Dec 2021 16:28:12: 20000000 INFO @ Wed, 08 Dec 2021 16:28:13: 14000000 INFO @ Wed, 08 Dec 2021 16:28:15: 10000000 INFO @ Wed, 08 Dec 2021 16:28:18: 21000000 INFO @ Wed, 08 Dec 2021 16:28:20: 15000000 INFO @ Wed, 08 Dec 2021 16:28:21: 11000000 INFO @ Wed, 08 Dec 2021 16:28:24: 22000000 INFO @ Wed, 08 Dec 2021 16:28:26: 16000000 INFO @ Wed, 08 Dec 2021 16:28:27: 12000000 INFO @ Wed, 08 Dec 2021 16:28:30: 23000000 INFO @ Wed, 08 Dec 2021 16:28:33: 17000000 INFO @ Wed, 08 Dec 2021 16:28:33: 13000000 INFO @ Wed, 08 Dec 2021 16:28:36: 24000000 INFO @ Wed, 08 Dec 2021 16:28:39: 14000000 INFO @ Wed, 08 Dec 2021 16:28:40: 18000000 INFO @ Wed, 08 Dec 2021 16:28:42: 25000000 INFO @ Wed, 08 Dec 2021 16:28:46: 15000000 INFO @ Wed, 08 Dec 2021 16:28:46: 19000000 INFO @ Wed, 08 Dec 2021 16:28:48: 26000000 INFO @ Wed, 08 Dec 2021 16:28:52: 16000000 INFO @ Wed, 08 Dec 2021 16:28:53: 20000000 INFO @ Wed, 08 Dec 2021 16:28:55: 27000000 INFO @ Wed, 08 Dec 2021 16:28:59: 17000000 INFO @ Wed, 08 Dec 2021 16:29:00: 21000000 INFO @ Wed, 08 Dec 2021 16:29:01: 28000000 INFO @ Wed, 08 Dec 2021 16:29:05: 18000000 INFO @ Wed, 08 Dec 2021 16:29:06: 22000000 INFO @ Wed, 08 Dec 2021 16:29:08: 29000000 INFO @ Wed, 08 Dec 2021 16:29:12: 19000000 INFO @ Wed, 08 Dec 2021 16:29:13: 23000000 INFO @ Wed, 08 Dec 2021 16:29:14: 30000000 INFO @ Wed, 08 Dec 2021 16:29:18: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 16:29:18: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 16:29:18: #1 total tags in treatment: 10366495 INFO @ Wed, 08 Dec 2021 16:29:18: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:29:18: #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 16:29:18: 20000000 INFO @ Wed, 08 Dec 2021 16:29:18: #1 tags after filtering in treatment: 9679285 INFO @ Wed, 08 Dec 2021 16:29:18: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 16:29:18: #1 finished! INFO @ Wed, 08 Dec 2021 16:29:18: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:29:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:29:19: #2 number of paired peaks: 459 WARNING @ Wed, 08 Dec 2021 16:29:19: Fewer paired peaks (459) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 459 pairs to build model! INFO @ Wed, 08 Dec 2021 16:29:19: start model_add_line... INFO @ Wed, 08 Dec 2021 16:29:19: start X-correlation... INFO @ Wed, 08 Dec 2021 16:29:19: end of X-cor INFO @ Wed, 08 Dec 2021 16:29:19: #2 finished! INFO @ Wed, 08 Dec 2021 16:29:19: #2 predicted fragment length is 157 bps INFO @ Wed, 08 Dec 2021 16:29:19: #2 alternative fragment length(s) may be 4,157 bps INFO @ Wed, 08 Dec 2021 16:29:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342590/SRX10342590.05_model.r INFO @ Wed, 08 Dec 2021 16:29:19: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:29:19: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:29:19: 24000000 INFO @ Wed, 08 Dec 2021 16:29:24: 21000000 INFO @ Wed, 08 Dec 2021 16:29:26: 25000000 INFO @ Wed, 08 Dec 2021 16:29:30: 22000000 INFO @ Wed, 08 Dec 2021 16:29:33: 26000000 INFO @ Wed, 08 Dec 2021 16:29:36: 23000000 INFO @ Wed, 08 Dec 2021 16:29:39: 27000000 INFO @ Wed, 08 Dec 2021 16:29:42: 24000000 INFO @ Wed, 08 Dec 2021 16:29:46: 28000000 INFO @ Wed, 08 Dec 2021 16:29:48: 25000000 INFO @ Wed, 08 Dec 2021 16:29:49: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:29:52: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 16:29:54: 26000000 INFO @ Wed, 08 Dec 2021 16:29:59: 30000000 INFO @ Wed, 08 Dec 2021 16:30:00: 27000000 INFO @ Wed, 08 Dec 2021 16:30:02: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 16:30:02: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 16:30:02: #1 total tags in treatment: 10366495 INFO @ Wed, 08 Dec 2021 16:30:02: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:30:02: #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 16:30:02: #1 tags after filtering in treatment: 9679285 INFO @ Wed, 08 Dec 2021 16:30:02: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 16:30:02: #1 finished! INFO @ Wed, 08 Dec 2021 16:30:02: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:30:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:30:03: #2 number of paired peaks: 459 WARNING @ Wed, 08 Dec 2021 16:30:03: Fewer paired peaks (459) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 459 pairs to build model! INFO @ Wed, 08 Dec 2021 16:30:03: start model_add_line... INFO @ Wed, 08 Dec 2021 16:30:03: start X-correlation... INFO @ Wed, 08 Dec 2021 16:30:03: end of X-cor INFO @ Wed, 08 Dec 2021 16:30:03: #2 finished! INFO @ Wed, 08 Dec 2021 16:30:03: #2 predicted fragment length is 157 bps INFO @ Wed, 08 Dec 2021 16:30:03: #2 alternative fragment length(s) may be 4,157 bps INFO @ Wed, 08 Dec 2021 16:30:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342590/SRX10342590.10_model.r INFO @ Wed, 08 Dec 2021 16:30:03: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:30:03: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:30:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342590/SRX10342590.05_peaks.xls INFO @ Wed, 08 Dec 2021 16:30:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342590/SRX10342590.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:30:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342590/SRX10342590.05_summits.bed INFO @ Wed, 08 Dec 2021 16:30:04: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4132 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 16:30:06: 28000000 INFO @ Wed, 08 Dec 2021 16:30:12: 29000000 INFO @ Wed, 08 Dec 2021 16:30:18: 30000000 INFO @ Wed, 08 Dec 2021 16:30:22: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 16:30:22: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 16:30:22: #1 total tags in treatment: 10366495 INFO @ Wed, 08 Dec 2021 16:30:22: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:30:22: #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 16:30:22: #1 tags after filtering in treatment: 9679285 INFO @ Wed, 08 Dec 2021 16:30:22: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 16:30:22: #1 finished! INFO @ Wed, 08 Dec 2021 16:30:22: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:30:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:30:23: #2 number of paired peaks: 459 WARNING @ Wed, 08 Dec 2021 16:30:23: Fewer paired peaks (459) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 459 pairs to build model! INFO @ Wed, 08 Dec 2021 16:30:23: start model_add_line... INFO @ Wed, 08 Dec 2021 16:30:23: start X-correlation... INFO @ Wed, 08 Dec 2021 16:30:23: end of X-cor INFO @ Wed, 08 Dec 2021 16:30:23: #2 finished! INFO @ Wed, 08 Dec 2021 16:30:23: #2 predicted fragment length is 157 bps INFO @ Wed, 08 Dec 2021 16:30:23: #2 alternative fragment length(s) may be 4,157 bps INFO @ Wed, 08 Dec 2021 16:30:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342590/SRX10342590.20_model.r INFO @ Wed, 08 Dec 2021 16:30:23: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:30:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:30:32: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:30:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342590/SRX10342590.10_peaks.xls INFO @ Wed, 08 Dec 2021 16:30:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342590/SRX10342590.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:30:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342590/SRX10342590.10_summits.bed INFO @ Wed, 08 Dec 2021 16:30:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1673 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 16:30:52: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:31:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342590/SRX10342590.20_peaks.xls INFO @ Wed, 08 Dec 2021 16:31:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342590/SRX10342590.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:31:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342590/SRX10342590.20_summits.bed INFO @ Wed, 08 Dec 2021 16:31:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (267 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。