Job ID = 14159130 SRX = SRX8976743 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18070562 spots for SRR12483287/SRR12483287.sra Written 18070562 spots for SRR12483287/SRR12483287.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159419 ("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: 00:24:54 18070562 reads; of these: 18070562 (100.00%) were paired; of these: 2132141 (11.80%) aligned concordantly 0 times 11334302 (62.72%) aligned concordantly exactly 1 time 4604119 (25.48%) aligned concordantly >1 times ---- 2132141 pairs aligned concordantly 0 times; of these: 1197386 (56.16%) aligned discordantly 1 time ---- 934755 pairs aligned 0 times concordantly or discordantly; of these: 1869510 mates make up the pairs; of these: 382394 (20.45%) aligned 0 times 454573 (24.32%) aligned exactly 1 time 1032543 (55.23%) aligned >1 times 98.94% overall alignment rate Time searching: 00:24:54 Overall time: 00:24:54 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] 1319381 / 17120426 = 0.0771 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 20:21:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976743/SRX8976743.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976743/SRX8976743.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976743/SRX8976743.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976743/SRX8976743.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 20:21:19: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:21:19: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:21:25: 1000000 INFO @ Wed, 08 Dec 2021 20:21:32: 2000000 INFO @ Wed, 08 Dec 2021 20:21:39: 3000000 INFO @ Wed, 08 Dec 2021 20:21:45: 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 20:21:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976743/SRX8976743.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976743/SRX8976743.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976743/SRX8976743.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976743/SRX8976743.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 20:21:49: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:21:49: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:21:52: 5000000 INFO @ Wed, 08 Dec 2021 20:21:55: 1000000 INFO @ Wed, 08 Dec 2021 20:21:59: 6000000 INFO @ Wed, 08 Dec 2021 20:22:01: 2000000 INFO @ Wed, 08 Dec 2021 20:22:05: 7000000 INFO @ Wed, 08 Dec 2021 20:22:07: 3000000 INFO @ Wed, 08 Dec 2021 20:22:12: 8000000 INFO @ Wed, 08 Dec 2021 20:22:12: 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 20:22:18: 9000000 INFO @ Wed, 08 Dec 2021 20:22:18: 5000000 INFO @ Wed, 08 Dec 2021 20:22:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976743/SRX8976743.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976743/SRX8976743.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976743/SRX8976743.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976743/SRX8976743.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 20:22:19: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:22:19: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:22:24: 10000000 INFO @ Wed, 08 Dec 2021 20:22:24: 6000000 INFO @ Wed, 08 Dec 2021 20:22:27: 1000000 INFO @ Wed, 08 Dec 2021 20:22:30: 11000000 INFO @ Wed, 08 Dec 2021 20:22:30: 7000000 INFO @ Wed, 08 Dec 2021 20:22:36: 8000000 INFO @ Wed, 08 Dec 2021 20:22:36: 12000000 INFO @ Wed, 08 Dec 2021 20:22:36: 2000000 INFO @ Wed, 08 Dec 2021 20:22:43: 9000000 INFO @ Wed, 08 Dec 2021 20:22:43: 13000000 INFO @ Wed, 08 Dec 2021 20:22:45: 3000000 INFO @ Wed, 08 Dec 2021 20:22:50: 10000000 INFO @ Wed, 08 Dec 2021 20:22:50: 14000000 INFO @ Wed, 08 Dec 2021 20:22:54: 4000000 INFO @ Wed, 08 Dec 2021 20:22:58: 11000000 INFO @ Wed, 08 Dec 2021 20:22:58: 15000000 INFO @ Wed, 08 Dec 2021 20:23:03: 5000000 INFO @ Wed, 08 Dec 2021 20:23:05: 12000000 INFO @ Wed, 08 Dec 2021 20:23:05: 16000000 INFO @ Wed, 08 Dec 2021 20:23:11: 6000000 INFO @ Wed, 08 Dec 2021 20:23:12: 13000000 INFO @ Wed, 08 Dec 2021 20:23:12: 17000000 INFO @ Wed, 08 Dec 2021 20:23:19: 14000000 INFO @ Wed, 08 Dec 2021 20:23:19: 18000000 INFO @ Wed, 08 Dec 2021 20:23:19: 7000000 INFO @ Wed, 08 Dec 2021 20:23:25: 15000000 INFO @ Wed, 08 Dec 2021 20:23:25: 19000000 INFO @ Wed, 08 Dec 2021 20:23:27: 8000000 INFO @ Wed, 08 Dec 2021 20:23:31: 16000000 INFO @ Wed, 08 Dec 2021 20:23:32: 20000000 INFO @ Wed, 08 Dec 2021 20:23:35: 9000000 INFO @ Wed, 08 Dec 2021 20:23:37: 17000000 INFO @ Wed, 08 Dec 2021 20:23:38: 21000000 INFO @ Wed, 08 Dec 2021 20:23:43: 10000000 INFO @ Wed, 08 Dec 2021 20:23:44: 18000000 INFO @ Wed, 08 Dec 2021 20:23:44: 22000000 INFO @ Wed, 08 Dec 2021 20:23:50: 19000000 INFO @ Wed, 08 Dec 2021 20:23:51: 11000000 INFO @ Wed, 08 Dec 2021 20:23:51: 23000000 INFO @ Wed, 08 Dec 2021 20:23:57: 20000000 INFO @ Wed, 08 Dec 2021 20:23:58: 24000000 INFO @ Wed, 08 Dec 2021 20:23:59: 12000000 INFO @ Wed, 08 Dec 2021 20:24:04: 21000000 INFO @ Wed, 08 Dec 2021 20:24:05: 25000000 INFO @ Wed, 08 Dec 2021 20:24:07: 13000000 INFO @ Wed, 08 Dec 2021 20:24:11: 22000000 INFO @ Wed, 08 Dec 2021 20:24:12: 26000000 INFO @ Wed, 08 Dec 2021 20:24:15: 14000000 INFO @ Wed, 08 Dec 2021 20:24:18: 23000000 INFO @ Wed, 08 Dec 2021 20:24:19: 27000000 INFO @ Wed, 08 Dec 2021 20:24:23: 15000000 INFO @ Wed, 08 Dec 2021 20:24:25: 24000000 INFO @ Wed, 08 Dec 2021 20:24:26: 28000000 INFO @ Wed, 08 Dec 2021 20:24:31: 16000000 INFO @ Wed, 08 Dec 2021 20:24:32: 25000000 INFO @ Wed, 08 Dec 2021 20:24:33: 29000000 INFO @ Wed, 08 Dec 2021 20:24:39: 17000000 INFO @ Wed, 08 Dec 2021 20:24:39: 26000000 INFO @ Wed, 08 Dec 2021 20:24:40: 30000000 INFO @ Wed, 08 Dec 2021 20:24:46: 27000000 INFO @ Wed, 08 Dec 2021 20:24:47: 18000000 INFO @ Wed, 08 Dec 2021 20:24:47: 31000000 INFO @ Wed, 08 Dec 2021 20:24:53: 28000000 INFO @ Wed, 08 Dec 2021 20:24:54: 32000000 INFO @ Wed, 08 Dec 2021 20:24:55: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 20:25:00: 29000000 INFO @ Wed, 08 Dec 2021 20:25:01: 33000000 INFO @ Wed, 08 Dec 2021 20:25:02: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 20:25:02: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 20:25:02: #1 total tags in treatment: 14675612 INFO @ Wed, 08 Dec 2021 20:25:02: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:25:02: #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 20:25:02: #1 tags after filtering in treatment: 11332672 INFO @ Wed, 08 Dec 2021 20:25:02: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 08 Dec 2021 20:25:02: #1 finished! INFO @ Wed, 08 Dec 2021 20:25:02: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:25:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:25:02: 20000000 INFO @ Wed, 08 Dec 2021 20:25:03: #2 number of paired peaks: 4093 INFO @ Wed, 08 Dec 2021 20:25:03: start model_add_line... INFO @ Wed, 08 Dec 2021 20:25:04: start X-correlation... INFO @ Wed, 08 Dec 2021 20:25:04: end of X-cor INFO @ Wed, 08 Dec 2021 20:25:04: #2 finished! INFO @ Wed, 08 Dec 2021 20:25:04: #2 predicted fragment length is 242 bps INFO @ Wed, 08 Dec 2021 20:25:04: #2 alternative fragment length(s) may be 1,201,230,242,261 bps INFO @ Wed, 08 Dec 2021 20:25:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976743/SRX8976743.05_model.r INFO @ Wed, 08 Dec 2021 20:25:04: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:25:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:25:06: 30000000 INFO @ Wed, 08 Dec 2021 20:25:10: 21000000 INFO @ Wed, 08 Dec 2021 20:25:12: 31000000 INFO @ Wed, 08 Dec 2021 20:25:18: 22000000 INFO @ Wed, 08 Dec 2021 20:25:18: 32000000 INFO @ Wed, 08 Dec 2021 20:25:24: 33000000 INFO @ Wed, 08 Dec 2021 20:25:25: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 20:25:25: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 20:25:25: #1 total tags in treatment: 14675612 INFO @ Wed, 08 Dec 2021 20:25:25: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:25:25: #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 20:25:25: #1 tags after filtering in treatment: 11332672 INFO @ Wed, 08 Dec 2021 20:25:25: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 08 Dec 2021 20:25:25: #1 finished! INFO @ Wed, 08 Dec 2021 20:25:25: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:25:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:25:25: 23000000 INFO @ Wed, 08 Dec 2021 20:25:26: #2 number of paired peaks: 4093 INFO @ Wed, 08 Dec 2021 20:25:26: start model_add_line... INFO @ Wed, 08 Dec 2021 20:25:27: start X-correlation... INFO @ Wed, 08 Dec 2021 20:25:27: end of X-cor INFO @ Wed, 08 Dec 2021 20:25:27: #2 finished! INFO @ Wed, 08 Dec 2021 20:25:27: #2 predicted fragment length is 242 bps INFO @ Wed, 08 Dec 2021 20:25:27: #2 alternative fragment length(s) may be 1,201,230,242,261 bps INFO @ Wed, 08 Dec 2021 20:25:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976743/SRX8976743.10_model.r INFO @ Wed, 08 Dec 2021 20:25:27: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:25:27: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:25:33: 24000000 INFO @ Wed, 08 Dec 2021 20:25:40: 25000000 INFO @ Wed, 08 Dec 2021 20:25:47: 26000000 INFO @ Wed, 08 Dec 2021 20:25:49: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:25:54: 27000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 20:26:02: 28000000 INFO @ Wed, 08 Dec 2021 20:26:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976743/SRX8976743.05_peaks.xls INFO @ Wed, 08 Dec 2021 20:26:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976743/SRX8976743.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:26:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976743/SRX8976743.05_summits.bed INFO @ Wed, 08 Dec 2021 20:26:03: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2105 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:26:09: 29000000 INFO @ Wed, 08 Dec 2021 20:26:12: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:26:16: 30000000 INFO @ Wed, 08 Dec 2021 20:26:25: 31000000 INFO @ Wed, 08 Dec 2021 20:26:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976743/SRX8976743.10_peaks.xls INFO @ Wed, 08 Dec 2021 20:26:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976743/SRX8976743.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:26:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976743/SRX8976743.10_summits.bed INFO @ Wed, 08 Dec 2021 20:26:26: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (930 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:26:32: 32000000 INFO @ Wed, 08 Dec 2021 20:26:40: 33000000 INFO @ Wed, 08 Dec 2021 20:26:41: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 20:26:41: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 20:26:41: #1 total tags in treatment: 14675612 INFO @ Wed, 08 Dec 2021 20:26:41: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:26:41: #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 20:26:41: #1 tags after filtering in treatment: 11332672 INFO @ Wed, 08 Dec 2021 20:26:41: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 08 Dec 2021 20:26:41: #1 finished! INFO @ Wed, 08 Dec 2021 20:26:41: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:26:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:26:43: #2 number of paired peaks: 4093 INFO @ Wed, 08 Dec 2021 20:26:43: start model_add_line... INFO @ Wed, 08 Dec 2021 20:26:43: start X-correlation... INFO @ Wed, 08 Dec 2021 20:26:43: end of X-cor INFO @ Wed, 08 Dec 2021 20:26:43: #2 finished! INFO @ Wed, 08 Dec 2021 20:26:43: #2 predicted fragment length is 242 bps INFO @ Wed, 08 Dec 2021 20:26:43: #2 alternative fragment length(s) may be 1,201,230,242,261 bps INFO @ Wed, 08 Dec 2021 20:26:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976743/SRX8976743.20_model.r INFO @ Wed, 08 Dec 2021 20:26:43: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:26:43: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:27:28: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:27:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976743/SRX8976743.20_peaks.xls INFO @ Wed, 08 Dec 2021 20:27:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976743/SRX8976743.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:27:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976743/SRX8976743.20_summits.bed INFO @ Wed, 08 Dec 2021 20:27:43: Done! pass1 - making usageList (7 chroms): 5 millis pass2 - checking and writing primary data (368 records, 4 fields): 93 millis CompletedMACS2peakCalling