Job ID = 14158262 SRX = SRX10342581 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9479932 spots for SRR13964618/SRR13964618.sra Written 9479932 spots for SRR13964618/SRR13964618.sra Read 10480923 spots for SRR13964619/SRR13964619.sra Written 10480923 spots for SRR13964619/SRR13964619.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158796 ("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: 00:14:06 19960855 reads; of these: 19960855 (100.00%) were paired; of these: 4937290 (24.73%) aligned concordantly 0 times 12917264 (64.71%) aligned concordantly exactly 1 time 2106301 (10.55%) aligned concordantly >1 times ---- 4937290 pairs aligned concordantly 0 times; of these: 3640618 (73.74%) aligned discordantly 1 time ---- 1296672 pairs aligned 0 times concordantly or discordantly; of these: 2593344 mates make up the pairs; of these: 1093653 (42.17%) aligned 0 times 585460 (22.58%) aligned exactly 1 time 914231 (35.25%) aligned >1 times 97.26% overall alignment rate Time searching: 00:14:06 Overall time: 00:14:06 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] 2251238 / 18651889 = 0.1207 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 15:52:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342581/SRX10342581.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342581/SRX10342581.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342581/SRX10342581.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342581/SRX10342581.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 15:52:23: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:52:23: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:52:27: 1000000 INFO @ Wed, 08 Dec 2021 15:52:30: 2000000 INFO @ Wed, 08 Dec 2021 15:52:34: 3000000 INFO @ Wed, 08 Dec 2021 15:52:38: 4000000 INFO @ Wed, 08 Dec 2021 15:52:42: 5000000 INFO @ Wed, 08 Dec 2021 15:52:45: 6000000 INFO @ Wed, 08 Dec 2021 15:52:49: 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 15:52:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342581/SRX10342581.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342581/SRX10342581.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342581/SRX10342581.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342581/SRX10342581.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 15:52:53: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:52:53: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:52:53: 8000000 INFO @ Wed, 08 Dec 2021 15:52:57: 9000000 INFO @ Wed, 08 Dec 2021 15:52:57: 1000000 INFO @ Wed, 08 Dec 2021 15:53:01: 10000000 INFO @ Wed, 08 Dec 2021 15:53:02: 2000000 INFO @ Wed, 08 Dec 2021 15:53:05: 11000000 INFO @ Wed, 08 Dec 2021 15:53:06: 3000000 INFO @ Wed, 08 Dec 2021 15:53:08: 12000000 INFO @ Wed, 08 Dec 2021 15:53:11: 4000000 INFO @ Wed, 08 Dec 2021 15:53:12: 13000000 INFO @ Wed, 08 Dec 2021 15:53:16: 5000000 INFO @ Wed, 08 Dec 2021 15:53:16: 14000000 INFO @ Wed, 08 Dec 2021 15:53:20: 15000000 INFO @ Wed, 08 Dec 2021 15:53:20: 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 15:53:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342581/SRX10342581.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342581/SRX10342581.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342581/SRX10342581.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342581/SRX10342581.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 15:53:23: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:53:23: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:53:24: 16000000 INFO @ Wed, 08 Dec 2021 15:53:25: 7000000 INFO @ Wed, 08 Dec 2021 15:53:27: 1000000 INFO @ Wed, 08 Dec 2021 15:53:28: 17000000 INFO @ Wed, 08 Dec 2021 15:53:30: 8000000 INFO @ Wed, 08 Dec 2021 15:53:31: 2000000 INFO @ Wed, 08 Dec 2021 15:53:32: 18000000 INFO @ Wed, 08 Dec 2021 15:53:34: 9000000 INFO @ Wed, 08 Dec 2021 15:53:35: 3000000 INFO @ Wed, 08 Dec 2021 15:53:36: 19000000 INFO @ Wed, 08 Dec 2021 15:53:39: 4000000 INFO @ Wed, 08 Dec 2021 15:53:39: 10000000 INFO @ Wed, 08 Dec 2021 15:53:40: 20000000 INFO @ Wed, 08 Dec 2021 15:53:43: 5000000 INFO @ Wed, 08 Dec 2021 15:53:44: 11000000 INFO @ Wed, 08 Dec 2021 15:53:44: 21000000 INFO @ Wed, 08 Dec 2021 15:53:47: 6000000 INFO @ Wed, 08 Dec 2021 15:53:48: 22000000 INFO @ Wed, 08 Dec 2021 15:53:49: 12000000 INFO @ Wed, 08 Dec 2021 15:53:51: 7000000 INFO @ Wed, 08 Dec 2021 15:53:52: 23000000 INFO @ Wed, 08 Dec 2021 15:53:53: 13000000 INFO @ Wed, 08 Dec 2021 15:53:55: 8000000 INFO @ Wed, 08 Dec 2021 15:53:56: 24000000 INFO @ Wed, 08 Dec 2021 15:53:58: 14000000 INFO @ Wed, 08 Dec 2021 15:53:59: 9000000 INFO @ Wed, 08 Dec 2021 15:54:00: 25000000 INFO @ Wed, 08 Dec 2021 15:54:03: 15000000 INFO @ Wed, 08 Dec 2021 15:54:03: 10000000 INFO @ Wed, 08 Dec 2021 15:54:04: 26000000 INFO @ Wed, 08 Dec 2021 15:54:07: 11000000 INFO @ Wed, 08 Dec 2021 15:54:07: 16000000 INFO @ Wed, 08 Dec 2021 15:54:08: 27000000 INFO @ Wed, 08 Dec 2021 15:54:11: 12000000 INFO @ Wed, 08 Dec 2021 15:54:12: 17000000 INFO @ Wed, 08 Dec 2021 15:54:12: 28000000 INFO @ Wed, 08 Dec 2021 15:54:15: 13000000 INFO @ Wed, 08 Dec 2021 15:54:16: 29000000 INFO @ Wed, 08 Dec 2021 15:54:17: 18000000 INFO @ Wed, 08 Dec 2021 15:54:19: 14000000 INFO @ Wed, 08 Dec 2021 15:54:20: 30000000 INFO @ Wed, 08 Dec 2021 15:54:21: 19000000 INFO @ Wed, 08 Dec 2021 15:54:23: 15000000 INFO @ Wed, 08 Dec 2021 15:54:24: 31000000 INFO @ Wed, 08 Dec 2021 15:54:26: 20000000 INFO @ Wed, 08 Dec 2021 15:54:27: 16000000 INFO @ Wed, 08 Dec 2021 15:54:28: 32000000 INFO @ Wed, 08 Dec 2021 15:54:30: 21000000 INFO @ Wed, 08 Dec 2021 15:54:31: 17000000 INFO @ Wed, 08 Dec 2021 15:54:32: 33000000 INFO @ Wed, 08 Dec 2021 15:54:35: 22000000 INFO @ Wed, 08 Dec 2021 15:54:35: 18000000 INFO @ Wed, 08 Dec 2021 15:54:36: 34000000 INFO @ Wed, 08 Dec 2021 15:54:38: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 15:54:38: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 15:54:38: #1 total tags in treatment: 13106272 INFO @ Wed, 08 Dec 2021 15:54:38: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:54:38: #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 15:54:38: #1 tags after filtering in treatment: 11740895 INFO @ Wed, 08 Dec 2021 15:54:38: #1 Redundant rate of treatment: 0.10 INFO @ Wed, 08 Dec 2021 15:54:38: #1 finished! INFO @ Wed, 08 Dec 2021 15:54:38: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:54:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:54:39: #2 number of paired peaks: 457 WARNING @ Wed, 08 Dec 2021 15:54:39: Fewer paired peaks (457) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 457 pairs to build model! INFO @ Wed, 08 Dec 2021 15:54:39: start model_add_line... INFO @ Wed, 08 Dec 2021 15:54:39: start X-correlation... INFO @ Wed, 08 Dec 2021 15:54:39: end of X-cor INFO @ Wed, 08 Dec 2021 15:54:39: #2 finished! INFO @ Wed, 08 Dec 2021 15:54:39: #2 predicted fragment length is 142 bps INFO @ Wed, 08 Dec 2021 15:54:39: #2 alternative fragment length(s) may be 3,96,122,142 bps INFO @ Wed, 08 Dec 2021 15:54:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342581/SRX10342581.05_model.r INFO @ Wed, 08 Dec 2021 15:54:39: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:54:39: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:54:39: 19000000 INFO @ Wed, 08 Dec 2021 15:54:39: 23000000 INFO @ Wed, 08 Dec 2021 15:54:43: 20000000 INFO @ Wed, 08 Dec 2021 15:54:44: 24000000 INFO @ Wed, 08 Dec 2021 15:54:47: 21000000 INFO @ Wed, 08 Dec 2021 15:54:48: 25000000 INFO @ Wed, 08 Dec 2021 15:54:51: 22000000 INFO @ Wed, 08 Dec 2021 15:54:53: 26000000 INFO @ Wed, 08 Dec 2021 15:54:55: 23000000 INFO @ Wed, 08 Dec 2021 15:54:57: 27000000 INFO @ Wed, 08 Dec 2021 15:54:59: 24000000 INFO @ Wed, 08 Dec 2021 15:55:01: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:55:02: 28000000 INFO @ Wed, 08 Dec 2021 15:55:02: 25000000 INFO @ Wed, 08 Dec 2021 15:55:06: 26000000 INFO @ Wed, 08 Dec 2021 15:55:06: 29000000 INFO @ Wed, 08 Dec 2021 15:55:10: 27000000 INFO @ Wed, 08 Dec 2021 15:55:11: 30000000 INFO @ Wed, 08 Dec 2021 15:55:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342581/SRX10342581.05_peaks.xls INFO @ Wed, 08 Dec 2021 15:55:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342581/SRX10342581.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:55:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342581/SRX10342581.05_summits.bed INFO @ Wed, 08 Dec 2021 15:55:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (406 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 15:55:14: 28000000 INFO @ Wed, 08 Dec 2021 15:55:15: 31000000 INFO @ Wed, 08 Dec 2021 15:55:18: 29000000 INFO @ Wed, 08 Dec 2021 15:55:20: 32000000 INFO @ Wed, 08 Dec 2021 15:55:22: 30000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 15:55:24: 33000000 INFO @ Wed, 08 Dec 2021 15:55:26: 31000000 INFO @ Wed, 08 Dec 2021 15:55:28: 34000000 INFO @ Wed, 08 Dec 2021 15:55:30: 32000000 INFO @ Wed, 08 Dec 2021 15:55:30: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 15:55:30: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 15:55:30: #1 total tags in treatment: 13106272 INFO @ Wed, 08 Dec 2021 15:55:30: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:55:30: #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 15:55:30: #1 tags after filtering in treatment: 11740895 INFO @ Wed, 08 Dec 2021 15:55:30: #1 Redundant rate of treatment: 0.10 INFO @ Wed, 08 Dec 2021 15:55:30: #1 finished! INFO @ Wed, 08 Dec 2021 15:55:30: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:55:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:55:31: #2 number of paired peaks: 457 WARNING @ Wed, 08 Dec 2021 15:55:31: Fewer paired peaks (457) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 457 pairs to build model! INFO @ Wed, 08 Dec 2021 15:55:31: start model_add_line... INFO @ Wed, 08 Dec 2021 15:55:31: start X-correlation... INFO @ Wed, 08 Dec 2021 15:55:31: end of X-cor INFO @ Wed, 08 Dec 2021 15:55:31: #2 finished! INFO @ Wed, 08 Dec 2021 15:55:31: #2 predicted fragment length is 142 bps INFO @ Wed, 08 Dec 2021 15:55:31: #2 alternative fragment length(s) may be 3,96,122,142 bps INFO @ Wed, 08 Dec 2021 15:55:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342581/SRX10342581.10_model.r INFO @ Wed, 08 Dec 2021 15:55:31: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:55:31: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:55:34: 33000000 INFO @ Wed, 08 Dec 2021 15:55:37: 34000000 INFO @ Wed, 08 Dec 2021 15:55:39: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 15:55:39: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 15:55:39: #1 total tags in treatment: 13106272 INFO @ Wed, 08 Dec 2021 15:55:39: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:55:39: #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 15:55:39: #1 tags after filtering in treatment: 11740895 INFO @ Wed, 08 Dec 2021 15:55:39: #1 Redundant rate of treatment: 0.10 INFO @ Wed, 08 Dec 2021 15:55:39: #1 finished! INFO @ Wed, 08 Dec 2021 15:55:39: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:55:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:55:40: #2 number of paired peaks: 457 WARNING @ Wed, 08 Dec 2021 15:55:40: Fewer paired peaks (457) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 457 pairs to build model! INFO @ Wed, 08 Dec 2021 15:55:40: start model_add_line... INFO @ Wed, 08 Dec 2021 15:55:40: start X-correlation... INFO @ Wed, 08 Dec 2021 15:55:40: end of X-cor INFO @ Wed, 08 Dec 2021 15:55:40: #2 finished! INFO @ Wed, 08 Dec 2021 15:55:40: #2 predicted fragment length is 142 bps INFO @ Wed, 08 Dec 2021 15:55:40: #2 alternative fragment length(s) may be 3,96,122,142 bps INFO @ Wed, 08 Dec 2021 15:55:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342581/SRX10342581.20_model.r INFO @ Wed, 08 Dec 2021 15:55:40: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:55:40: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:55:53: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:56:01: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:56:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342581/SRX10342581.10_peaks.xls INFO @ Wed, 08 Dec 2021 15:56:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342581/SRX10342581.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:56:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342581/SRX10342581.10_summits.bed INFO @ Wed, 08 Dec 2021 15:56:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (312 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 15:56:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342581/SRX10342581.20_peaks.xls INFO @ Wed, 08 Dec 2021 15:56:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342581/SRX10342581.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:56:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342581/SRX10342581.20_summits.bed INFO @ Wed, 08 Dec 2021 15:56:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (208 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。