Job ID = 14159080 SRX = SRX8976729 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12407286 spots for SRR12483273/SRR12483273.sra Written 12407286 spots for SRR12483273/SRR12483273.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159315 ("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: 00:09:23 12407286 reads; of these: 12407286 (100.00%) were paired; of these: 855420 (6.89%) aligned concordantly 0 times 10060504 (81.09%) aligned concordantly exactly 1 time 1491362 (12.02%) aligned concordantly >1 times ---- 855420 pairs aligned concordantly 0 times; of these: 632756 (73.97%) aligned discordantly 1 time ---- 222664 pairs aligned 0 times concordantly or discordantly; of these: 445328 mates make up the pairs; of these: 125427 (28.17%) aligned 0 times 143009 (32.11%) aligned exactly 1 time 176892 (39.72%) aligned >1 times 99.49% overall alignment rate Time searching: 00:09:23 Overall time: 00:09:23 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] 323304 / 12154311 = 0.0266 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 19:06:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976729/SRX8976729.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976729/SRX8976729.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976729/SRX8976729.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976729/SRX8976729.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 19:06:19: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:06:19: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:06:25: 1000000 INFO @ Wed, 08 Dec 2021 19:06:31: 2000000 INFO @ Wed, 08 Dec 2021 19:06:36: 3000000 INFO @ Wed, 08 Dec 2021 19:06:42: 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 19:06:48: 5000000 INFO @ Wed, 08 Dec 2021 19:06:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976729/SRX8976729.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976729/SRX8976729.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976729/SRX8976729.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976729/SRX8976729.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 19:06:49: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:06:49: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:06:55: 6000000 INFO @ Wed, 08 Dec 2021 19:06:55: 1000000 INFO @ Wed, 08 Dec 2021 19:07:01: 7000000 INFO @ Wed, 08 Dec 2021 19:07:01: 2000000 INFO @ Wed, 08 Dec 2021 19:07:08: 3000000 INFO @ Wed, 08 Dec 2021 19:07:08: 8000000 INFO @ Wed, 08 Dec 2021 19:07:14: 4000000 INFO @ Wed, 08 Dec 2021 19:07:15: 9000000 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 19:07:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976729/SRX8976729.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976729/SRX8976729.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976729/SRX8976729.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976729/SRX8976729.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 19:07:19: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:07:19: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:07:21: 5000000 INFO @ Wed, 08 Dec 2021 19:07:22: 10000000 INFO @ Wed, 08 Dec 2021 19:07:25: 1000000 INFO @ Wed, 08 Dec 2021 19:07:27: 6000000 INFO @ Wed, 08 Dec 2021 19:07:28: 11000000 INFO @ Wed, 08 Dec 2021 19:07:31: 2000000 INFO @ Wed, 08 Dec 2021 19:07:33: 7000000 INFO @ Wed, 08 Dec 2021 19:07:35: 12000000 INFO @ Wed, 08 Dec 2021 19:07:37: 3000000 INFO @ Wed, 08 Dec 2021 19:07:40: 8000000 INFO @ Wed, 08 Dec 2021 19:07:41: 13000000 INFO @ Wed, 08 Dec 2021 19:07:43: 4000000 INFO @ Wed, 08 Dec 2021 19:07:46: 9000000 INFO @ Wed, 08 Dec 2021 19:07:48: 14000000 INFO @ Wed, 08 Dec 2021 19:07:49: 5000000 INFO @ Wed, 08 Dec 2021 19:07:52: 10000000 INFO @ Wed, 08 Dec 2021 19:07:55: 6000000 INFO @ Wed, 08 Dec 2021 19:07:55: 15000000 INFO @ Wed, 08 Dec 2021 19:07:58: 11000000 INFO @ Wed, 08 Dec 2021 19:08:01: 7000000 INFO @ Wed, 08 Dec 2021 19:08:02: 16000000 INFO @ Wed, 08 Dec 2021 19:08:04: 12000000 INFO @ Wed, 08 Dec 2021 19:08:07: 8000000 INFO @ Wed, 08 Dec 2021 19:08:08: 17000000 INFO @ Wed, 08 Dec 2021 19:08:10: 13000000 INFO @ Wed, 08 Dec 2021 19:08:13: 9000000 INFO @ Wed, 08 Dec 2021 19:08:15: 18000000 INFO @ Wed, 08 Dec 2021 19:08:16: 14000000 INFO @ Wed, 08 Dec 2021 19:08:19: 10000000 INFO @ Wed, 08 Dec 2021 19:08:22: 19000000 INFO @ Wed, 08 Dec 2021 19:08:22: 15000000 INFO @ Wed, 08 Dec 2021 19:08:25: 11000000 INFO @ Wed, 08 Dec 2021 19:08:28: 16000000 INFO @ Wed, 08 Dec 2021 19:08:28: 20000000 INFO @ Wed, 08 Dec 2021 19:08:31: 12000000 INFO @ Wed, 08 Dec 2021 19:08:34: 17000000 INFO @ Wed, 08 Dec 2021 19:08:35: 21000000 INFO @ Wed, 08 Dec 2021 19:08:37: 13000000 INFO @ Wed, 08 Dec 2021 19:08:40: 18000000 INFO @ Wed, 08 Dec 2021 19:08:42: 22000000 INFO @ Wed, 08 Dec 2021 19:08:43: 14000000 INFO @ Wed, 08 Dec 2021 19:08:46: 19000000 INFO @ Wed, 08 Dec 2021 19:08:48: 23000000 INFO @ Wed, 08 Dec 2021 19:08:49: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 19:08:52: 20000000 INFO @ Wed, 08 Dec 2021 19:08:55: 24000000 INFO @ Wed, 08 Dec 2021 19:08:55: 16000000 INFO @ Wed, 08 Dec 2021 19:08:55: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 19:08:55: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 19:08:55: #1 total tags in treatment: 11241172 INFO @ Wed, 08 Dec 2021 19:08:55: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:08:55: #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 19:08:55: #1 tags after filtering in treatment: 10562838 INFO @ Wed, 08 Dec 2021 19:08:55: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 19:08:55: #1 finished! INFO @ Wed, 08 Dec 2021 19:08:55: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:08:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:08:56: #2 number of paired peaks: 374 WARNING @ Wed, 08 Dec 2021 19:08:56: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Wed, 08 Dec 2021 19:08:56: start model_add_line... INFO @ Wed, 08 Dec 2021 19:08:56: start X-correlation... INFO @ Wed, 08 Dec 2021 19:08:56: end of X-cor INFO @ Wed, 08 Dec 2021 19:08:56: #2 finished! INFO @ Wed, 08 Dec 2021 19:08:56: #2 predicted fragment length is 145 bps INFO @ Wed, 08 Dec 2021 19:08:56: #2 alternative fragment length(s) may be 4,145 bps INFO @ Wed, 08 Dec 2021 19:08:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976729/SRX8976729.05_model.r INFO @ Wed, 08 Dec 2021 19:08:56: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:08:56: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:08:58: 21000000 INFO @ Wed, 08 Dec 2021 19:09:00: 17000000 INFO @ Wed, 08 Dec 2021 19:09:04: 22000000 INFO @ Wed, 08 Dec 2021 19:09:06: 18000000 INFO @ Wed, 08 Dec 2021 19:09:09: 23000000 INFO @ Wed, 08 Dec 2021 19:09:12: 19000000 INFO @ Wed, 08 Dec 2021 19:09:14: 24000000 INFO @ Wed, 08 Dec 2021 19:09:15: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 19:09:15: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 19:09:15: #1 total tags in treatment: 11241172 INFO @ Wed, 08 Dec 2021 19:09:15: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:09:15: #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 19:09:15: #1 tags after filtering in treatment: 10562838 INFO @ Wed, 08 Dec 2021 19:09:15: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 19:09:15: #1 finished! INFO @ Wed, 08 Dec 2021 19:09:15: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:09:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:09:16: #2 number of paired peaks: 374 WARNING @ Wed, 08 Dec 2021 19:09:16: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Wed, 08 Dec 2021 19:09:16: start model_add_line... INFO @ Wed, 08 Dec 2021 19:09:16: start X-correlation... INFO @ Wed, 08 Dec 2021 19:09:16: end of X-cor INFO @ Wed, 08 Dec 2021 19:09:16: #2 finished! INFO @ Wed, 08 Dec 2021 19:09:16: #2 predicted fragment length is 145 bps INFO @ Wed, 08 Dec 2021 19:09:16: #2 alternative fragment length(s) may be 4,145 bps INFO @ Wed, 08 Dec 2021 19:09:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976729/SRX8976729.10_model.r INFO @ Wed, 08 Dec 2021 19:09:16: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:09:16: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:09:16: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:09:17: 20000000 INFO @ Wed, 08 Dec 2021 19:09:22: 21000000 INFO @ Wed, 08 Dec 2021 19:09:27: 22000000 INFO @ Wed, 08 Dec 2021 19:09:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976729/SRX8976729.05_peaks.xls INFO @ Wed, 08 Dec 2021 19:09:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976729/SRX8976729.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:09:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976729/SRX8976729.05_summits.bed INFO @ Wed, 08 Dec 2021 19:09:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (335 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 19:09:32: 23000000 INFO @ Wed, 08 Dec 2021 19:09:36: 24000000 INFO @ Wed, 08 Dec 2021 19:09:37: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 19:09:37: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 19:09:37: #1 total tags in treatment: 11241172 INFO @ Wed, 08 Dec 2021 19:09:37: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:09:37: #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 19:09:37: #1 tags after filtering in treatment: 10562838 INFO @ Wed, 08 Dec 2021 19:09:37: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 19:09:37: #1 finished! INFO @ Wed, 08 Dec 2021 19:09:37: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:09:37: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:09:37: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:09:38: #2 number of paired peaks: 374 WARNING @ Wed, 08 Dec 2021 19:09:38: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Wed, 08 Dec 2021 19:09:38: start model_add_line... INFO @ Wed, 08 Dec 2021 19:09:38: start X-correlation... INFO @ Wed, 08 Dec 2021 19:09:38: end of X-cor INFO @ Wed, 08 Dec 2021 19:09:38: #2 finished! INFO @ Wed, 08 Dec 2021 19:09:38: #2 predicted fragment length is 145 bps INFO @ Wed, 08 Dec 2021 19:09:38: #2 alternative fragment length(s) may be 4,145 bps INFO @ Wed, 08 Dec 2021 19:09:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976729/SRX8976729.20_model.r INFO @ Wed, 08 Dec 2021 19:09:38: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:09:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 19:09:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976729/SRX8976729.10_peaks.xls INFO @ Wed, 08 Dec 2021 19:09:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976729/SRX8976729.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:09:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976729/SRX8976729.10_summits.bed INFO @ Wed, 08 Dec 2021 19:09:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (236 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 19:09:58: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:10:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976729/SRX8976729.20_peaks.xls INFO @ Wed, 08 Dec 2021 19:10:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976729/SRX8976729.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:10:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976729/SRX8976729.20_summits.bed INFO @ Wed, 08 Dec 2021 19:10:08: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (168 records, 4 fields): 10 millis CompletedMACS2peakCalling