Job ID = 14159065 SRX = SRX8976725 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12998729 spots for SRR12483269/SRR12483269.sra Written 12998729 spots for SRR12483269/SRR12483269.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159313 ("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: 00:09:49 12998729 reads; of these: 12998729 (100.00%) were paired; of these: 306386 (2.36%) aligned concordantly 0 times 10996519 (84.60%) aligned concordantly exactly 1 time 1695824 (13.05%) aligned concordantly >1 times ---- 306386 pairs aligned concordantly 0 times; of these: 171381 (55.94%) aligned discordantly 1 time ---- 135005 pairs aligned 0 times concordantly or discordantly; of these: 270010 mates make up the pairs; of these: 119712 (44.34%) aligned 0 times 79761 (29.54%) aligned exactly 1 time 70537 (26.12%) aligned >1 times 99.54% overall alignment rate Time searching: 00:09:49 Overall time: 00:09:49 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] 347132 / 12824779 = 0.0271 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 19:04:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976725/SRX8976725.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976725/SRX8976725.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976725/SRX8976725.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976725/SRX8976725.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 19:04:24: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:04:24: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:04:28: 1000000 INFO @ Wed, 08 Dec 2021 19:04:32: 2000000 INFO @ Wed, 08 Dec 2021 19:04:37: 3000000 INFO @ Wed, 08 Dec 2021 19:04:41: 4000000 INFO @ Wed, 08 Dec 2021 19:04:46: 5000000 INFO @ Wed, 08 Dec 2021 19:04:50: 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 19:04:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976725/SRX8976725.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976725/SRX8976725.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976725/SRX8976725.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976725/SRX8976725.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 19:04:53: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:04:53: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:04:55: 7000000 INFO @ Wed, 08 Dec 2021 19:04:59: 1000000 INFO @ Wed, 08 Dec 2021 19:05:00: 8000000 INFO @ Wed, 08 Dec 2021 19:05:05: 9000000 INFO @ Wed, 08 Dec 2021 19:05:05: 2000000 INFO @ Wed, 08 Dec 2021 19:05:10: 10000000 INFO @ Wed, 08 Dec 2021 19:05:10: 3000000 INFO @ Wed, 08 Dec 2021 19:05:15: 11000000 INFO @ Wed, 08 Dec 2021 19:05:16: 4000000 INFO @ Wed, 08 Dec 2021 19:05:20: 12000000 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 19:05:22: 5000000 INFO @ Wed, 08 Dec 2021 19:05:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976725/SRX8976725.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976725/SRX8976725.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976725/SRX8976725.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976725/SRX8976725.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 19:05:23: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:05:23: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:05:25: 13000000 INFO @ Wed, 08 Dec 2021 19:05:28: 6000000 INFO @ Wed, 08 Dec 2021 19:05:29: 1000000 INFO @ Wed, 08 Dec 2021 19:05:30: 14000000 INFO @ Wed, 08 Dec 2021 19:05:33: 7000000 INFO @ Wed, 08 Dec 2021 19:05:34: 2000000 INFO @ Wed, 08 Dec 2021 19:05:35: 15000000 INFO @ Wed, 08 Dec 2021 19:05:39: 3000000 INFO @ Wed, 08 Dec 2021 19:05:39: 8000000 INFO @ Wed, 08 Dec 2021 19:05:40: 16000000 INFO @ Wed, 08 Dec 2021 19:05:44: 4000000 INFO @ Wed, 08 Dec 2021 19:05:45: 9000000 INFO @ Wed, 08 Dec 2021 19:05:45: 17000000 INFO @ Wed, 08 Dec 2021 19:05:49: 5000000 INFO @ Wed, 08 Dec 2021 19:05:50: 18000000 INFO @ Wed, 08 Dec 2021 19:05:50: 10000000 INFO @ Wed, 08 Dec 2021 19:05:54: 6000000 INFO @ Wed, 08 Dec 2021 19:05:55: 19000000 INFO @ Wed, 08 Dec 2021 19:05:56: 11000000 INFO @ Wed, 08 Dec 2021 19:05:59: 7000000 INFO @ Wed, 08 Dec 2021 19:06:00: 20000000 INFO @ Wed, 08 Dec 2021 19:06:02: 12000000 INFO @ Wed, 08 Dec 2021 19:06:04: 8000000 INFO @ Wed, 08 Dec 2021 19:06:05: 21000000 INFO @ Wed, 08 Dec 2021 19:06:08: 13000000 INFO @ Wed, 08 Dec 2021 19:06:10: 9000000 INFO @ Wed, 08 Dec 2021 19:06:11: 22000000 INFO @ Wed, 08 Dec 2021 19:06:13: 14000000 INFO @ Wed, 08 Dec 2021 19:06:15: 10000000 INFO @ Wed, 08 Dec 2021 19:06:16: 23000000 INFO @ Wed, 08 Dec 2021 19:06:19: 15000000 INFO @ Wed, 08 Dec 2021 19:06:20: 11000000 INFO @ Wed, 08 Dec 2021 19:06:21: 24000000 INFO @ Wed, 08 Dec 2021 19:06:25: 16000000 INFO @ Wed, 08 Dec 2021 19:06:25: 12000000 INFO @ Wed, 08 Dec 2021 19:06:26: 25000000 INFO @ Wed, 08 Dec 2021 19:06:27: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 19:06:27: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 19:06:27: #1 total tags in treatment: 12347923 INFO @ Wed, 08 Dec 2021 19:06:27: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:06:27: #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 19:06:27: #1 tags after filtering in treatment: 11561566 INFO @ Wed, 08 Dec 2021 19:06:27: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 19:06:27: #1 finished! INFO @ Wed, 08 Dec 2021 19:06:27: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:06:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:06:28: #2 number of paired peaks: 308 WARNING @ Wed, 08 Dec 2021 19:06:28: Fewer paired peaks (308) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 308 pairs to build model! INFO @ Wed, 08 Dec 2021 19:06:28: start model_add_line... INFO @ Wed, 08 Dec 2021 19:06:28: start X-correlation... INFO @ Wed, 08 Dec 2021 19:06:28: end of X-cor INFO @ Wed, 08 Dec 2021 19:06:28: #2 finished! INFO @ Wed, 08 Dec 2021 19:06:28: #2 predicted fragment length is 157 bps INFO @ Wed, 08 Dec 2021 19:06:28: #2 alternative fragment length(s) may be 4,138,157,182 bps INFO @ Wed, 08 Dec 2021 19:06:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976725/SRX8976725.05_model.r INFO @ Wed, 08 Dec 2021 19:06:28: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:06:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:06:30: 13000000 INFO @ Wed, 08 Dec 2021 19:06:30: 17000000 INFO @ Wed, 08 Dec 2021 19:06:35: 14000000 INFO @ Wed, 08 Dec 2021 19:06:36: 18000000 INFO @ Wed, 08 Dec 2021 19:06:40: 15000000 INFO @ Wed, 08 Dec 2021 19:06:42: 19000000 INFO @ Wed, 08 Dec 2021 19:06:45: 16000000 INFO @ Wed, 08 Dec 2021 19:06:48: 20000000 INFO @ Wed, 08 Dec 2021 19:06:50: 17000000 INFO @ Wed, 08 Dec 2021 19:06:51: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:06:53: 21000000 INFO @ Wed, 08 Dec 2021 19:06:55: 18000000 INFO @ Wed, 08 Dec 2021 19:06:59: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 19:07:00: 19000000 INFO @ Wed, 08 Dec 2021 19:07:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976725/SRX8976725.05_peaks.xls INFO @ Wed, 08 Dec 2021 19:07:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976725/SRX8976725.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:07:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976725/SRX8976725.05_summits.bed INFO @ Wed, 08 Dec 2021 19:07:01: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (310 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 19:07:05: 23000000 INFO @ Wed, 08 Dec 2021 19:07:05: 20000000 INFO @ Wed, 08 Dec 2021 19:07:11: 21000000 INFO @ Wed, 08 Dec 2021 19:07:11: 24000000 INFO @ Wed, 08 Dec 2021 19:07:16: 22000000 INFO @ Wed, 08 Dec 2021 19:07:16: 25000000 INFO @ Wed, 08 Dec 2021 19:07:17: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 19:07:17: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 19:07:17: #1 total tags in treatment: 12347923 INFO @ Wed, 08 Dec 2021 19:07:17: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:07:17: #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 19:07:18: #1 tags after filtering in treatment: 11561566 INFO @ Wed, 08 Dec 2021 19:07:18: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 19:07:18: #1 finished! INFO @ Wed, 08 Dec 2021 19:07:18: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:07:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:07:18: #2 number of paired peaks: 308 WARNING @ Wed, 08 Dec 2021 19:07:18: Fewer paired peaks (308) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 308 pairs to build model! INFO @ Wed, 08 Dec 2021 19:07:18: start model_add_line... INFO @ Wed, 08 Dec 2021 19:07:18: start X-correlation... INFO @ Wed, 08 Dec 2021 19:07:18: end of X-cor INFO @ Wed, 08 Dec 2021 19:07:18: #2 finished! INFO @ Wed, 08 Dec 2021 19:07:18: #2 predicted fragment length is 157 bps INFO @ Wed, 08 Dec 2021 19:07:18: #2 alternative fragment length(s) may be 4,138,157,182 bps INFO @ Wed, 08 Dec 2021 19:07:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976725/SRX8976725.10_model.r INFO @ Wed, 08 Dec 2021 19:07:19: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:07:19: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:07:21: 23000000 INFO @ Wed, 08 Dec 2021 19:07:25: 24000000 INFO @ Wed, 08 Dec 2021 19:07:30: 25000000 INFO @ Wed, 08 Dec 2021 19:07:31: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 19:07:31: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 19:07:31: #1 total tags in treatment: 12347923 INFO @ Wed, 08 Dec 2021 19:07:31: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:07:31: #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 19:07:31: #1 tags after filtering in treatment: 11561566 INFO @ Wed, 08 Dec 2021 19:07:31: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 19:07:31: #1 finished! INFO @ Wed, 08 Dec 2021 19:07:31: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:07:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:07:32: #2 number of paired peaks: 308 WARNING @ Wed, 08 Dec 2021 19:07:32: Fewer paired peaks (308) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 308 pairs to build model! INFO @ Wed, 08 Dec 2021 19:07:32: start model_add_line... INFO @ Wed, 08 Dec 2021 19:07:32: start X-correlation... INFO @ Wed, 08 Dec 2021 19:07:32: end of X-cor INFO @ Wed, 08 Dec 2021 19:07:32: #2 finished! INFO @ Wed, 08 Dec 2021 19:07:32: #2 predicted fragment length is 157 bps INFO @ Wed, 08 Dec 2021 19:07:32: #2 alternative fragment length(s) may be 4,138,157,182 bps INFO @ Wed, 08 Dec 2021 19:07:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976725/SRX8976725.20_model.r INFO @ Wed, 08 Dec 2021 19:07:32: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:07:32: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:07:40: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 19:07:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976725/SRX8976725.10_peaks.xls INFO @ Wed, 08 Dec 2021 19:07:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976725/SRX8976725.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:07:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976725/SRX8976725.10_summits.bed INFO @ Wed, 08 Dec 2021 19:07:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (241 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 19:07:54: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:08:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976725/SRX8976725.20_peaks.xls INFO @ Wed, 08 Dec 2021 19:08:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976725/SRX8976725.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:08:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976725/SRX8976725.20_summits.bed INFO @ Wed, 08 Dec 2021 19:08:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (162 records, 4 fields): 1 millis CompletedMACS2peakCalling