Job ID = 14158905 SRX = SRX8976713 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14404796 spots for SRR12483317/SRR12483317.sra Written 14404796 spots for SRR12483317/SRR12483317.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159271 ("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: 00:15:08 14404796 reads; of these: 14404796 (100.00%) were paired; of these: 223189 (1.55%) aligned concordantly 0 times 12304324 (85.42%) aligned concordantly exactly 1 time 1877283 (13.03%) aligned concordantly >1 times ---- 223189 pairs aligned concordantly 0 times; of these: 78380 (35.12%) aligned discordantly 1 time ---- 144809 pairs aligned 0 times concordantly or discordantly; of these: 289618 mates make up the pairs; of these: 188884 (65.22%) aligned 0 times 62847 (21.70%) aligned exactly 1 time 37887 (13.08%) aligned >1 times 99.34% overall alignment rate Time searching: 00:15:08 Overall time: 00:15:08 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] 205857 / 14242843 = 0.0145 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 18:42:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976713/SRX8976713.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976713/SRX8976713.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976713/SRX8976713.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976713/SRX8976713.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 18:42:55: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:42:55: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:43:03: 1000000 INFO @ Wed, 08 Dec 2021 18:43:11: 2000000 INFO @ Wed, 08 Dec 2021 18:43:18: 3000000 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 18:43:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976713/SRX8976713.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976713/SRX8976713.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976713/SRX8976713.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976713/SRX8976713.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 18:43:25: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:43:25: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:43:26: 4000000 INFO @ Wed, 08 Dec 2021 18:43:32: 1000000 INFO @ Wed, 08 Dec 2021 18:43:34: 5000000 INFO @ Wed, 08 Dec 2021 18:43:39: 2000000 INFO @ Wed, 08 Dec 2021 18:43:42: 6000000 INFO @ Wed, 08 Dec 2021 18:43:47: 3000000 INFO @ Wed, 08 Dec 2021 18:43:50: 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 18:43:54: 4000000 INFO @ Wed, 08 Dec 2021 18:43:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976713/SRX8976713.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976713/SRX8976713.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976713/SRX8976713.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976713/SRX8976713.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 18:43:55: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:43:55: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:43:58: 8000000 INFO @ Wed, 08 Dec 2021 18:44:01: 5000000 INFO @ Wed, 08 Dec 2021 18:44:04: 1000000 INFO @ Wed, 08 Dec 2021 18:44:06: 9000000 INFO @ Wed, 08 Dec 2021 18:44:08: 6000000 INFO @ Wed, 08 Dec 2021 18:44:12: 2000000 INFO @ Wed, 08 Dec 2021 18:44:15: 10000000 INFO @ Wed, 08 Dec 2021 18:44:15: 7000000 INFO @ Wed, 08 Dec 2021 18:44:20: 3000000 INFO @ Wed, 08 Dec 2021 18:44:22: 8000000 INFO @ Wed, 08 Dec 2021 18:44:23: 11000000 INFO @ Wed, 08 Dec 2021 18:44:28: 4000000 INFO @ Wed, 08 Dec 2021 18:44:30: 9000000 INFO @ Wed, 08 Dec 2021 18:44:31: 12000000 INFO @ Wed, 08 Dec 2021 18:44:36: 5000000 INFO @ Wed, 08 Dec 2021 18:44:38: 10000000 INFO @ Wed, 08 Dec 2021 18:44:40: 13000000 INFO @ Wed, 08 Dec 2021 18:44:45: 6000000 INFO @ Wed, 08 Dec 2021 18:44:46: 11000000 INFO @ Wed, 08 Dec 2021 18:44:48: 14000000 INFO @ Wed, 08 Dec 2021 18:44:54: 7000000 INFO @ Wed, 08 Dec 2021 18:44:55: 12000000 INFO @ Wed, 08 Dec 2021 18:44:57: 15000000 INFO @ Wed, 08 Dec 2021 18:45:03: 8000000 INFO @ Wed, 08 Dec 2021 18:45:04: 13000000 INFO @ Wed, 08 Dec 2021 18:45:06: 16000000 INFO @ Wed, 08 Dec 2021 18:45:11: 14000000 INFO @ Wed, 08 Dec 2021 18:45:12: 9000000 INFO @ Wed, 08 Dec 2021 18:45:15: 17000000 INFO @ Wed, 08 Dec 2021 18:45:18: 15000000 INFO @ Wed, 08 Dec 2021 18:45:20: 10000000 INFO @ Wed, 08 Dec 2021 18:45:23: 18000000 INFO @ Wed, 08 Dec 2021 18:45:25: 16000000 INFO @ Wed, 08 Dec 2021 18:45:29: 11000000 INFO @ Wed, 08 Dec 2021 18:45:32: 19000000 INFO @ Wed, 08 Dec 2021 18:45:32: 17000000 INFO @ Wed, 08 Dec 2021 18:45:38: 12000000 INFO @ Wed, 08 Dec 2021 18:45:39: 18000000 INFO @ Wed, 08 Dec 2021 18:45:41: 20000000 INFO @ Wed, 08 Dec 2021 18:45:46: 19000000 INFO @ Wed, 08 Dec 2021 18:45:47: 13000000 INFO @ Wed, 08 Dec 2021 18:45:50: 21000000 INFO @ Wed, 08 Dec 2021 18:45:53: 20000000 INFO @ Wed, 08 Dec 2021 18:45:56: 14000000 INFO @ Wed, 08 Dec 2021 18:45:59: 22000000 INFO @ Wed, 08 Dec 2021 18:46:00: 21000000 INFO @ Wed, 08 Dec 2021 18:46:05: 15000000 INFO @ Wed, 08 Dec 2021 18:46:07: 23000000 INFO @ Wed, 08 Dec 2021 18:46:07: 22000000 INFO @ Wed, 08 Dec 2021 18:46:13: 16000000 INFO @ Wed, 08 Dec 2021 18:46:14: 23000000 INFO @ Wed, 08 Dec 2021 18:46:16: 24000000 INFO @ Wed, 08 Dec 2021 18:46:22: 17000000 INFO @ Wed, 08 Dec 2021 18:46:22: 24000000 INFO @ Wed, 08 Dec 2021 18:46:24: 25000000 INFO @ Wed, 08 Dec 2021 18:46:29: 25000000 INFO @ Wed, 08 Dec 2021 18:46:29: 18000000 INFO @ Wed, 08 Dec 2021 18:46:32: 26000000 INFO @ Wed, 08 Dec 2021 18:46:36: 26000000 INFO @ Wed, 08 Dec 2021 18:46:38: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:46:40: 27000000 INFO @ Wed, 08 Dec 2021 18:46:43: 27000000 INFO @ Wed, 08 Dec 2021 18:46:46: 20000000 INFO @ Wed, 08 Dec 2021 18:46:47: 28000000 INFO @ Wed, 08 Dec 2021 18:46:49: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:46:49: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:46:49: #1 total tags in treatment: 13976324 INFO @ Wed, 08 Dec 2021 18:46:49: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:46:49: #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 18:46:49: #1 tags after filtering in treatment: 13039905 INFO @ Wed, 08 Dec 2021 18:46:49: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 18:46:49: #1 finished! INFO @ Wed, 08 Dec 2021 18:46:49: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:46:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:46:50: 28000000 INFO @ Wed, 08 Dec 2021 18:46:50: #2 number of paired peaks: 304 WARNING @ Wed, 08 Dec 2021 18:46:50: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Wed, 08 Dec 2021 18:46:50: start model_add_line... INFO @ Wed, 08 Dec 2021 18:46:51: start X-correlation... INFO @ Wed, 08 Dec 2021 18:46:51: end of X-cor INFO @ Wed, 08 Dec 2021 18:46:51: #2 finished! INFO @ Wed, 08 Dec 2021 18:46:51: #2 predicted fragment length is 157 bps INFO @ Wed, 08 Dec 2021 18:46:51: #2 alternative fragment length(s) may be 4,157 bps INFO @ Wed, 08 Dec 2021 18:46:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976713/SRX8976713.05_model.r INFO @ Wed, 08 Dec 2021 18:46:51: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:46:51: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:46:51: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:46:51: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:46:51: #1 total tags in treatment: 13976324 INFO @ Wed, 08 Dec 2021 18:46:51: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:46:51: #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 18:46:52: #1 tags after filtering in treatment: 13039905 INFO @ Wed, 08 Dec 2021 18:46:52: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 18:46:52: #1 finished! INFO @ Wed, 08 Dec 2021 18:46:52: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:46:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:46:53: #2 number of paired peaks: 304 WARNING @ Wed, 08 Dec 2021 18:46:53: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Wed, 08 Dec 2021 18:46:53: start model_add_line... INFO @ Wed, 08 Dec 2021 18:46:53: start X-correlation... INFO @ Wed, 08 Dec 2021 18:46:53: end of X-cor INFO @ Wed, 08 Dec 2021 18:46:53: #2 finished! INFO @ Wed, 08 Dec 2021 18:46:53: #2 predicted fragment length is 157 bps INFO @ Wed, 08 Dec 2021 18:46:53: #2 alternative fragment length(s) may be 4,157 bps INFO @ Wed, 08 Dec 2021 18:46:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976713/SRX8976713.10_model.r INFO @ Wed, 08 Dec 2021 18:46:53: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:46:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:46:54: 21000000 INFO @ Wed, 08 Dec 2021 18:47:01: 22000000 INFO @ Wed, 08 Dec 2021 18:47:09: 23000000 INFO @ Wed, 08 Dec 2021 18:47:17: 24000000 INFO @ Wed, 08 Dec 2021 18:47:24: 25000000 INFO @ Wed, 08 Dec 2021 18:47:26: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:47:28: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:47:32: 26000000 INFO @ Wed, 08 Dec 2021 18:47:39: 27000000 INFO @ Wed, 08 Dec 2021 18:47:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976713/SRX8976713.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:47:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976713/SRX8976713.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:47:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976713/SRX8976713.05_summits.bed INFO @ Wed, 08 Dec 2021 18:47:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (342 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:47:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976713/SRX8976713.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:47:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976713/SRX8976713.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:47:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976713/SRX8976713.10_summits.bed INFO @ Wed, 08 Dec 2021 18:47:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (264 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:47:47: 28000000 INFO @ Wed, 08 Dec 2021 18:47:48: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:47:48: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:47:48: #1 total tags in treatment: 13976324 INFO @ Wed, 08 Dec 2021 18:47:48: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:47:48: #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 18:47:48: #1 tags after filtering in treatment: 13039905 INFO @ Wed, 08 Dec 2021 18:47:48: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 18:47:48: #1 finished! INFO @ Wed, 08 Dec 2021 18:47:48: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:47:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:47:50: #2 number of paired peaks: 304 WARNING @ Wed, 08 Dec 2021 18:47:50: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Wed, 08 Dec 2021 18:47:50: start model_add_line... INFO @ Wed, 08 Dec 2021 18:47:50: start X-correlation... INFO @ Wed, 08 Dec 2021 18:47:50: end of X-cor INFO @ Wed, 08 Dec 2021 18:47:50: #2 finished! INFO @ Wed, 08 Dec 2021 18:47:50: #2 predicted fragment length is 157 bps INFO @ Wed, 08 Dec 2021 18:47:50: #2 alternative fragment length(s) may be 4,157 bps INFO @ Wed, 08 Dec 2021 18:47:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976713/SRX8976713.20_model.r INFO @ Wed, 08 Dec 2021 18:47:50: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:47:50: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:48:25: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:48:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976713/SRX8976713.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:48:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976713/SRX8976713.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:48:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976713/SRX8976713.20_summits.bed INFO @ Wed, 08 Dec 2021 18:48:40: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (186 records, 4 fields): 2 millis CompletedMACS2peakCalling