Job ID = 14159436 SRX = SRX8976696 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16593452 spots for SRR12483300/SRR12483300.sra Written 16593452 spots for SRR12483300/SRR12483300.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159637 ("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: 00:12:56 16593452 reads; of these: 16593452 (100.00%) were paired; of these: 1137973 (6.86%) aligned concordantly 0 times 12860203 (77.50%) aligned concordantly exactly 1 time 2595276 (15.64%) aligned concordantly >1 times ---- 1137973 pairs aligned concordantly 0 times; of these: 595905 (52.37%) aligned discordantly 1 time ---- 542068 pairs aligned 0 times concordantly or discordantly; of these: 1084136 mates make up the pairs; of these: 660610 (60.93%) aligned 0 times 173279 (15.98%) aligned exactly 1 time 250247 (23.08%) aligned >1 times 98.01% overall alignment rate Time searching: 00:12:56 Overall time: 00:12:56 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] 1993087 / 16041783 = 0.1242 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 22:08:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976696/SRX8976696.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976696/SRX8976696.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976696/SRX8976696.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976696/SRX8976696.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 22:08:10: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:08:10: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:08:15: 1000000 INFO @ Wed, 08 Dec 2021 22:08:19: 2000000 INFO @ Wed, 08 Dec 2021 22:08:24: 3000000 INFO @ Wed, 08 Dec 2021 22:08:28: 4000000 INFO @ Wed, 08 Dec 2021 22:08:33: 5000000 INFO @ Wed, 08 Dec 2021 22:08:37: 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 22:08:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976696/SRX8976696.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976696/SRX8976696.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976696/SRX8976696.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976696/SRX8976696.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 22:08:40: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:08:40: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:08:42: 7000000 INFO @ Wed, 08 Dec 2021 22:08:45: 1000000 INFO @ Wed, 08 Dec 2021 22:08:47: 8000000 INFO @ Wed, 08 Dec 2021 22:08:51: 2000000 INFO @ Wed, 08 Dec 2021 22:08:53: 9000000 INFO @ Wed, 08 Dec 2021 22:08:56: 3000000 INFO @ Wed, 08 Dec 2021 22:08:58: 10000000 INFO @ Wed, 08 Dec 2021 22:09:01: 4000000 INFO @ Wed, 08 Dec 2021 22:09:03: 11000000 INFO @ Wed, 08 Dec 2021 22:09:06: 5000000 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 22:09:08: 12000000 INFO @ Wed, 08 Dec 2021 22:09:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976696/SRX8976696.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976696/SRX8976696.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976696/SRX8976696.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976696/SRX8976696.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 22:09:10: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:09:10: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:09:12: 6000000 INFO @ Wed, 08 Dec 2021 22:09:14: 13000000 INFO @ Wed, 08 Dec 2021 22:09:15: 1000000 INFO @ Wed, 08 Dec 2021 22:09:17: 7000000 INFO @ Wed, 08 Dec 2021 22:09:19: 14000000 INFO @ Wed, 08 Dec 2021 22:09:21: 2000000 INFO @ Wed, 08 Dec 2021 22:09:22: 8000000 INFO @ Wed, 08 Dec 2021 22:09:24: 15000000 INFO @ Wed, 08 Dec 2021 22:09:26: 3000000 INFO @ Wed, 08 Dec 2021 22:09:28: 9000000 INFO @ Wed, 08 Dec 2021 22:09:29: 16000000 INFO @ Wed, 08 Dec 2021 22:09:31: 4000000 INFO @ Wed, 08 Dec 2021 22:09:33: 10000000 INFO @ Wed, 08 Dec 2021 22:09:35: 17000000 INFO @ Wed, 08 Dec 2021 22:09:37: 5000000 INFO @ Wed, 08 Dec 2021 22:09:38: 11000000 INFO @ Wed, 08 Dec 2021 22:09:40: 18000000 INFO @ Wed, 08 Dec 2021 22:09:42: 6000000 INFO @ Wed, 08 Dec 2021 22:09:44: 12000000 INFO @ Wed, 08 Dec 2021 22:09:45: 19000000 INFO @ Wed, 08 Dec 2021 22:09:47: 7000000 INFO @ Wed, 08 Dec 2021 22:09:49: 13000000 INFO @ Wed, 08 Dec 2021 22:09:50: 20000000 INFO @ Wed, 08 Dec 2021 22:09:52: 8000000 INFO @ Wed, 08 Dec 2021 22:09:54: 14000000 INFO @ Wed, 08 Dec 2021 22:09:56: 21000000 INFO @ Wed, 08 Dec 2021 22:09:58: 9000000 INFO @ Wed, 08 Dec 2021 22:10:00: 15000000 INFO @ Wed, 08 Dec 2021 22:10:01: 22000000 INFO @ Wed, 08 Dec 2021 22:10:04: 10000000 INFO @ Wed, 08 Dec 2021 22:10:06: 16000000 INFO @ Wed, 08 Dec 2021 22:10:07: 23000000 INFO @ Wed, 08 Dec 2021 22:10:09: 11000000 INFO @ Wed, 08 Dec 2021 22:10:11: 17000000 INFO @ Wed, 08 Dec 2021 22:10:12: 24000000 INFO @ Wed, 08 Dec 2021 22:10:15: 12000000 INFO @ Wed, 08 Dec 2021 22:10:17: 18000000 INFO @ Wed, 08 Dec 2021 22:10:18: 25000000 INFO @ Wed, 08 Dec 2021 22:10:20: 13000000 INFO @ Wed, 08 Dec 2021 22:10:23: 19000000 INFO @ Wed, 08 Dec 2021 22:10:23: 26000000 INFO @ Wed, 08 Dec 2021 22:10:26: 14000000 INFO @ Wed, 08 Dec 2021 22:10:28: 20000000 INFO @ Wed, 08 Dec 2021 22:10:28: 27000000 INFO @ Wed, 08 Dec 2021 22:10:31: 15000000 INFO @ Wed, 08 Dec 2021 22:10:34: 21000000 INFO @ Wed, 08 Dec 2021 22:10:34: 28000000 INFO @ Wed, 08 Dec 2021 22:10:37: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 22:10:37: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 22:10:37: #1 total tags in treatment: 13511075 INFO @ Wed, 08 Dec 2021 22:10:37: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:10:37: #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 22:10:37: 16000000 INFO @ Wed, 08 Dec 2021 22:10:37: #1 tags after filtering in treatment: 12134452 INFO @ Wed, 08 Dec 2021 22:10:37: #1 Redundant rate of treatment: 0.10 INFO @ Wed, 08 Dec 2021 22:10:37: #1 finished! INFO @ Wed, 08 Dec 2021 22:10:37: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:10:37: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:10:38: #2 number of paired peaks: 1232 INFO @ Wed, 08 Dec 2021 22:10:38: start model_add_line... INFO @ Wed, 08 Dec 2021 22:10:38: start X-correlation... INFO @ Wed, 08 Dec 2021 22:10:38: end of X-cor INFO @ Wed, 08 Dec 2021 22:10:38: #2 finished! INFO @ Wed, 08 Dec 2021 22:10:38: #2 predicted fragment length is 192 bps INFO @ Wed, 08 Dec 2021 22:10:38: #2 alternative fragment length(s) may be 2,175,192,219 bps INFO @ Wed, 08 Dec 2021 22:10:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976696/SRX8976696.05_model.r INFO @ Wed, 08 Dec 2021 22:10:38: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:10:38: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:10:39: 22000000 INFO @ Wed, 08 Dec 2021 22:10:42: 17000000 INFO @ Wed, 08 Dec 2021 22:10:44: 23000000 INFO @ Wed, 08 Dec 2021 22:10:48: 18000000 INFO @ Wed, 08 Dec 2021 22:10:50: 24000000 INFO @ Wed, 08 Dec 2021 22:10:53: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 22:10:55: 25000000 INFO @ Wed, 08 Dec 2021 22:10:58: 20000000 INFO @ Wed, 08 Dec 2021 22:11:01: 26000000 INFO @ Wed, 08 Dec 2021 22:11:04: 21000000 INFO @ Wed, 08 Dec 2021 22:11:06: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:11:06: 27000000 INFO @ Wed, 08 Dec 2021 22:11:09: 22000000 INFO @ Wed, 08 Dec 2021 22:11:12: 28000000 INFO @ Wed, 08 Dec 2021 22:11:14: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 22:11:14: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 22:11:14: #1 total tags in treatment: 13511075 INFO @ Wed, 08 Dec 2021 22:11:14: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:11:14: #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 22:11:15: #1 tags after filtering in treatment: 12134452 INFO @ Wed, 08 Dec 2021 22:11:15: #1 Redundant rate of treatment: 0.10 INFO @ Wed, 08 Dec 2021 22:11:15: #1 finished! INFO @ Wed, 08 Dec 2021 22:11:15: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:11:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:11:15: 23000000 INFO @ Wed, 08 Dec 2021 22:11:16: #2 number of paired peaks: 1232 INFO @ Wed, 08 Dec 2021 22:11:16: start model_add_line... INFO @ Wed, 08 Dec 2021 22:11:16: start X-correlation... INFO @ Wed, 08 Dec 2021 22:11:16: end of X-cor INFO @ Wed, 08 Dec 2021 22:11:16: #2 finished! INFO @ Wed, 08 Dec 2021 22:11:16: #2 predicted fragment length is 192 bps INFO @ Wed, 08 Dec 2021 22:11:16: #2 alternative fragment length(s) may be 2,175,192,219 bps INFO @ Wed, 08 Dec 2021 22:11:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976696/SRX8976696.10_model.r INFO @ Wed, 08 Dec 2021 22:11:16: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:11:16: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:11:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976696/SRX8976696.05_peaks.xls INFO @ Wed, 08 Dec 2021 22:11:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976696/SRX8976696.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:11:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976696/SRX8976696.05_summits.bed INFO @ Wed, 08 Dec 2021 22:11:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1091 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:11:20: 24000000 INFO @ Wed, 08 Dec 2021 22:11:25: 25000000 INFO @ Wed, 08 Dec 2021 22:11:30: 26000000 INFO @ Wed, 08 Dec 2021 22:11:35: 27000000 INFO @ Wed, 08 Dec 2021 22:11:39: 28000000 INFO @ Wed, 08 Dec 2021 22:11:42: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 22:11:42: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 22:11:42: #1 total tags in treatment: 13511075 INFO @ Wed, 08 Dec 2021 22:11:42: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:11:42: #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 22:11:42: #1 tags after filtering in treatment: 12134452 INFO @ Wed, 08 Dec 2021 22:11:42: #1 Redundant rate of treatment: 0.10 INFO @ Wed, 08 Dec 2021 22:11:42: #1 finished! INFO @ Wed, 08 Dec 2021 22:11:42: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:11:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:11:43: #2 number of paired peaks: 1232 INFO @ Wed, 08 Dec 2021 22:11:43: start model_add_line... INFO @ Wed, 08 Dec 2021 22:11:43: start X-correlation... INFO @ Wed, 08 Dec 2021 22:11:43: end of X-cor INFO @ Wed, 08 Dec 2021 22:11:43: #2 finished! INFO @ Wed, 08 Dec 2021 22:11:43: #2 predicted fragment length is 192 bps INFO @ Wed, 08 Dec 2021 22:11:43: #2 alternative fragment length(s) may be 2,175,192,219 bps INFO @ Wed, 08 Dec 2021 22:11:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976696/SRX8976696.20_model.r INFO @ Wed, 08 Dec 2021 22:11:43: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:11:43: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:11:44: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 22:11:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976696/SRX8976696.10_peaks.xls INFO @ Wed, 08 Dec 2021 22:11:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976696/SRX8976696.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:11:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976696/SRX8976696.10_summits.bed INFO @ Wed, 08 Dec 2021 22:11:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (490 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:12:13: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:12:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976696/SRX8976696.20_peaks.xls INFO @ Wed, 08 Dec 2021 22:12:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976696/SRX8976696.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:12:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976696/SRX8976696.20_summits.bed INFO @ Wed, 08 Dec 2021 22:12:25: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (198 records, 4 fields): 2 millis CompletedMACS2peakCalling