Job ID = 14158862 SRX = SRX8976711 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13788149 spots for SRR12483315/SRR12483315.sra Written 13788149 spots for SRR12483315/SRR12483315.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159239 ("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: 00:11:03 13788149 reads; of these: 13788149 (100.00%) were paired; of these: 270348 (1.96%) aligned concordantly 0 times 11718997 (84.99%) aligned concordantly exactly 1 time 1798804 (13.05%) aligned concordantly >1 times ---- 270348 pairs aligned concordantly 0 times; of these: 84552 (31.28%) aligned discordantly 1 time ---- 185796 pairs aligned 0 times concordantly or discordantly; of these: 371592 mates make up the pairs; of these: 234492 (63.10%) aligned 0 times 94354 (25.39%) aligned exactly 1 time 42746 (11.50%) aligned >1 times 99.15% overall alignment rate Time searching: 00:11:03 Overall time: 00:11:03 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] 192119 / 13586947 = 0.0141 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 18:27:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976711/SRX8976711.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976711/SRX8976711.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976711/SRX8976711.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976711/SRX8976711.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 18:27:43: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:27:43: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:27:48: 1000000 INFO @ Wed, 08 Dec 2021 18:27:53: 2000000 INFO @ Wed, 08 Dec 2021 18:27:58: 3000000 INFO @ Wed, 08 Dec 2021 18:28:03: 4000000 INFO @ Wed, 08 Dec 2021 18:28:08: 5000000 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 18:28:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976711/SRX8976711.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976711/SRX8976711.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976711/SRX8976711.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976711/SRX8976711.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 18:28:13: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:28:13: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:28:13: 6000000 INFO @ Wed, 08 Dec 2021 18:28:19: 7000000 INFO @ Wed, 08 Dec 2021 18:28:20: 1000000 INFO @ Wed, 08 Dec 2021 18:28:25: 8000000 INFO @ Wed, 08 Dec 2021 18:28:26: 2000000 INFO @ Wed, 08 Dec 2021 18:28:31: 9000000 INFO @ Wed, 08 Dec 2021 18:28:33: 3000000 INFO @ Wed, 08 Dec 2021 18:28:37: 10000000 INFO @ Wed, 08 Dec 2021 18:28:40: 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 18:28:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976711/SRX8976711.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976711/SRX8976711.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976711/SRX8976711.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976711/SRX8976711.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 18:28:43: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:28:43: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:28:43: 11000000 INFO @ Wed, 08 Dec 2021 18:28:47: 5000000 INFO @ Wed, 08 Dec 2021 18:28:49: 12000000 INFO @ Wed, 08 Dec 2021 18:28:49: 1000000 INFO @ Wed, 08 Dec 2021 18:28:54: 6000000 INFO @ Wed, 08 Dec 2021 18:28:56: 13000000 INFO @ Wed, 08 Dec 2021 18:28:56: 2000000 INFO @ Wed, 08 Dec 2021 18:29:01: 7000000 INFO @ Wed, 08 Dec 2021 18:29:02: 14000000 INFO @ Wed, 08 Dec 2021 18:29:02: 3000000 INFO @ Wed, 08 Dec 2021 18:29:07: 8000000 INFO @ Wed, 08 Dec 2021 18:29:08: 15000000 INFO @ Wed, 08 Dec 2021 18:29:08: 4000000 INFO @ Wed, 08 Dec 2021 18:29:14: 9000000 INFO @ Wed, 08 Dec 2021 18:29:15: 16000000 INFO @ Wed, 08 Dec 2021 18:29:15: 5000000 INFO @ Wed, 08 Dec 2021 18:29:21: 17000000 INFO @ Wed, 08 Dec 2021 18:29:21: 6000000 INFO @ Wed, 08 Dec 2021 18:29:21: 10000000 INFO @ Wed, 08 Dec 2021 18:29:27: 18000000 INFO @ Wed, 08 Dec 2021 18:29:27: 7000000 INFO @ Wed, 08 Dec 2021 18:29:28: 11000000 INFO @ Wed, 08 Dec 2021 18:29:34: 19000000 INFO @ Wed, 08 Dec 2021 18:29:34: 8000000 INFO @ Wed, 08 Dec 2021 18:29:35: 12000000 INFO @ Wed, 08 Dec 2021 18:29:40: 20000000 INFO @ Wed, 08 Dec 2021 18:29:40: 9000000 INFO @ Wed, 08 Dec 2021 18:29:42: 13000000 INFO @ Wed, 08 Dec 2021 18:29:46: 21000000 INFO @ Wed, 08 Dec 2021 18:29:46: 10000000 INFO @ Wed, 08 Dec 2021 18:29:49: 14000000 INFO @ Wed, 08 Dec 2021 18:29:53: 22000000 INFO @ Wed, 08 Dec 2021 18:29:53: 11000000 INFO @ Wed, 08 Dec 2021 18:29:56: 15000000 INFO @ Wed, 08 Dec 2021 18:29:59: 23000000 INFO @ Wed, 08 Dec 2021 18:29:59: 12000000 INFO @ Wed, 08 Dec 2021 18:30:02: 16000000 INFO @ Wed, 08 Dec 2021 18:30:05: 24000000 INFO @ Wed, 08 Dec 2021 18:30:06: 13000000 INFO @ Wed, 08 Dec 2021 18:30:09: 17000000 INFO @ Wed, 08 Dec 2021 18:30:12: 25000000 INFO @ Wed, 08 Dec 2021 18:30:12: 14000000 INFO @ Wed, 08 Dec 2021 18:30:16: 18000000 INFO @ Wed, 08 Dec 2021 18:30:18: 26000000 INFO @ Wed, 08 Dec 2021 18:30:18: 15000000 INFO @ Wed, 08 Dec 2021 18:30:23: 19000000 INFO @ Wed, 08 Dec 2021 18:30:24: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:30:24: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:30:24: #1 total tags in treatment: 13326264 INFO @ Wed, 08 Dec 2021 18:30:24: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:30:24: #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 18:30:24: #1 tags after filtering in treatment: 12468055 INFO @ Wed, 08 Dec 2021 18:30:24: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 18:30:24: #1 finished! INFO @ Wed, 08 Dec 2021 18:30:24: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:30:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:30:24: 16000000 INFO @ Wed, 08 Dec 2021 18:30:25: #2 number of paired peaks: 306 WARNING @ Wed, 08 Dec 2021 18:30:25: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Wed, 08 Dec 2021 18:30:25: start model_add_line... INFO @ Wed, 08 Dec 2021 18:30:25: start X-correlation... INFO @ Wed, 08 Dec 2021 18:30:25: end of X-cor INFO @ Wed, 08 Dec 2021 18:30:25: #2 finished! INFO @ Wed, 08 Dec 2021 18:30:25: #2 predicted fragment length is 151 bps INFO @ Wed, 08 Dec 2021 18:30:25: #2 alternative fragment length(s) may be 4,151 bps INFO @ Wed, 08 Dec 2021 18:30:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976711/SRX8976711.05_model.r INFO @ Wed, 08 Dec 2021 18:30:25: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:30:25: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:30:30: 20000000 INFO @ Wed, 08 Dec 2021 18:30:30: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:30:36: 18000000 INFO @ Wed, 08 Dec 2021 18:30:37: 21000000 INFO @ Wed, 08 Dec 2021 18:30:42: 19000000 INFO @ Wed, 08 Dec 2021 18:30:43: 22000000 INFO @ Wed, 08 Dec 2021 18:30:48: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:30:48: 20000000 INFO @ Wed, 08 Dec 2021 18:30:50: 23000000 INFO @ Wed, 08 Dec 2021 18:30:54: 21000000 INFO @ Wed, 08 Dec 2021 18:30:57: 24000000 INFO @ Wed, 08 Dec 2021 18:30:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976711/SRX8976711.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:30:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976711/SRX8976711.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:30:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976711/SRX8976711.05_summits.bed INFO @ Wed, 08 Dec 2021 18:30:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (351 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:31:00: 22000000 INFO @ Wed, 08 Dec 2021 18:31:04: 25000000 INFO @ Wed, 08 Dec 2021 18:31:06: 23000000 INFO @ Wed, 08 Dec 2021 18:31:10: 26000000 INFO @ Wed, 08 Dec 2021 18:31:12: 24000000 INFO @ Wed, 08 Dec 2021 18:31:17: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:31:17: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:31:17: #1 total tags in treatment: 13326264 INFO @ Wed, 08 Dec 2021 18:31:17: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:31:17: #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 18:31:17: #1 tags after filtering in treatment: 12468055 INFO @ Wed, 08 Dec 2021 18:31:17: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 18:31:17: #1 finished! INFO @ Wed, 08 Dec 2021 18:31:17: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:31:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:31:17: 25000000 INFO @ Wed, 08 Dec 2021 18:31:18: #2 number of paired peaks: 306 WARNING @ Wed, 08 Dec 2021 18:31:18: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Wed, 08 Dec 2021 18:31:18: start model_add_line... INFO @ Wed, 08 Dec 2021 18:31:18: start X-correlation... INFO @ Wed, 08 Dec 2021 18:31:18: end of X-cor INFO @ Wed, 08 Dec 2021 18:31:18: #2 finished! INFO @ Wed, 08 Dec 2021 18:31:18: #2 predicted fragment length is 151 bps INFO @ Wed, 08 Dec 2021 18:31:18: #2 alternative fragment length(s) may be 4,151 bps INFO @ Wed, 08 Dec 2021 18:31:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976711/SRX8976711.10_model.r INFO @ Wed, 08 Dec 2021 18:31:18: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:31:18: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:31:23: 26000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:31:28: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:31:28: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:31:28: #1 total tags in treatment: 13326264 INFO @ Wed, 08 Dec 2021 18:31:28: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:31:28: #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 18:31:28: #1 tags after filtering in treatment: 12468055 INFO @ Wed, 08 Dec 2021 18:31:28: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 18:31:28: #1 finished! INFO @ Wed, 08 Dec 2021 18:31:28: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:31:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:31:29: #2 number of paired peaks: 306 WARNING @ Wed, 08 Dec 2021 18:31:29: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Wed, 08 Dec 2021 18:31:29: start model_add_line... INFO @ Wed, 08 Dec 2021 18:31:29: start X-correlation... INFO @ Wed, 08 Dec 2021 18:31:29: end of X-cor INFO @ Wed, 08 Dec 2021 18:31:29: #2 finished! INFO @ Wed, 08 Dec 2021 18:31:29: #2 predicted fragment length is 151 bps INFO @ Wed, 08 Dec 2021 18:31:29: #2 alternative fragment length(s) may be 4,151 bps INFO @ Wed, 08 Dec 2021 18:31:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976711/SRX8976711.20_model.r INFO @ Wed, 08 Dec 2021 18:31:29: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:31:29: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:31:40: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:31:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976711/SRX8976711.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:31:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976711/SRX8976711.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:31:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976711/SRX8976711.10_summits.bed INFO @ Wed, 08 Dec 2021 18:31:51: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (270 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:31:53: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:32:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976711/SRX8976711.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:32:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976711/SRX8976711.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:32:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976711/SRX8976711.20_summits.bed INFO @ Wed, 08 Dec 2021 18:32:04: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (194 records, 4 fields): 1 millis CompletedMACS2peakCalling