Job ID = 14160445 SRX = SRX8582580 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13458653 spots for SRR12054160/SRR12054160.sra Written 13458653 spots for SRR12054160/SRR12054160.sra Read 13365375 spots for SRR12054161/SRR12054161.sra Written 13365375 spots for SRR12054161/SRR12054161.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160631 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:21:36 26824028 reads; of these: 26824028 (100.00%) were paired; of these: 4213209 (15.71%) aligned concordantly 0 times 19147660 (71.38%) aligned concordantly exactly 1 time 3463159 (12.91%) aligned concordantly >1 times ---- 4213209 pairs aligned concordantly 0 times; of these: 1835137 (43.56%) aligned discordantly 1 time ---- 2378072 pairs aligned 0 times concordantly or discordantly; of these: 4756144 mates make up the pairs; of these: 3243880 (68.20%) aligned 0 times 939436 (19.75%) aligned exactly 1 time 572828 (12.04%) aligned >1 times 93.95% overall alignment rate Time searching: 00:21:37 Overall time: 00:21:37 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 24 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] 6745849 / 24434577 = 0.2761 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 @ Thu, 09 Dec 2021 03:05:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8582580/SRX8582580.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8582580/SRX8582580.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8582580/SRX8582580.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8582580/SRX8582580.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 @ Thu, 09 Dec 2021 03:05:49: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:05:49: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:05:55: 1000000 INFO @ Thu, 09 Dec 2021 03:06:02: 2000000 INFO @ Thu, 09 Dec 2021 03:06:08: 3000000 INFO @ Thu, 09 Dec 2021 03:06:14: 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 @ Thu, 09 Dec 2021 03:06:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8582580/SRX8582580.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8582580/SRX8582580.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8582580/SRX8582580.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8582580/SRX8582580.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 @ Thu, 09 Dec 2021 03:06:18: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:06:18: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:06:21: 5000000 INFO @ Thu, 09 Dec 2021 03:06:24: 1000000 INFO @ Thu, 09 Dec 2021 03:06:28: 6000000 INFO @ Thu, 09 Dec 2021 03:06:31: 2000000 INFO @ Thu, 09 Dec 2021 03:06:35: 7000000 INFO @ Thu, 09 Dec 2021 03:06:37: 3000000 INFO @ Thu, 09 Dec 2021 03:06:42: 8000000 INFO @ Thu, 09 Dec 2021 03:06:43: 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 @ Thu, 09 Dec 2021 03:06:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8582580/SRX8582580.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8582580/SRX8582580.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8582580/SRX8582580.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8582580/SRX8582580.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 @ Thu, 09 Dec 2021 03:06:48: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:06:48: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:06:49: 9000000 INFO @ Thu, 09 Dec 2021 03:06:50: 5000000 INFO @ Thu, 09 Dec 2021 03:06:55: 1000000 INFO @ Thu, 09 Dec 2021 03:06:56: 10000000 INFO @ Thu, 09 Dec 2021 03:06:56: 6000000 INFO @ Thu, 09 Dec 2021 03:07:02: 2000000 INFO @ Thu, 09 Dec 2021 03:07:03: 7000000 INFO @ Thu, 09 Dec 2021 03:07:03: 11000000 INFO @ Thu, 09 Dec 2021 03:07:09: 3000000 INFO @ Thu, 09 Dec 2021 03:07:09: 8000000 INFO @ Thu, 09 Dec 2021 03:07:10: 12000000 INFO @ Thu, 09 Dec 2021 03:07:16: 9000000 INFO @ Thu, 09 Dec 2021 03:07:16: 4000000 INFO @ Thu, 09 Dec 2021 03:07:18: 13000000 INFO @ Thu, 09 Dec 2021 03:07:22: 10000000 INFO @ Thu, 09 Dec 2021 03:07:24: 5000000 INFO @ Thu, 09 Dec 2021 03:07:25: 14000000 INFO @ Thu, 09 Dec 2021 03:07:29: 11000000 INFO @ Thu, 09 Dec 2021 03:07:31: 6000000 INFO @ Thu, 09 Dec 2021 03:07:33: 15000000 INFO @ Thu, 09 Dec 2021 03:07:35: 12000000 INFO @ Thu, 09 Dec 2021 03:07:39: 7000000 INFO @ Thu, 09 Dec 2021 03:07:40: 16000000 INFO @ Thu, 09 Dec 2021 03:07:42: 13000000 INFO @ Thu, 09 Dec 2021 03:07:46: 8000000 INFO @ Thu, 09 Dec 2021 03:07:48: 17000000 INFO @ Thu, 09 Dec 2021 03:07:48: 14000000 INFO @ Thu, 09 Dec 2021 03:07:53: 9000000 INFO @ Thu, 09 Dec 2021 03:07:55: 15000000 INFO @ Thu, 09 Dec 2021 03:07:56: 18000000 INFO @ Thu, 09 Dec 2021 03:08:00: 10000000 INFO @ Thu, 09 Dec 2021 03:08:01: 16000000 INFO @ Thu, 09 Dec 2021 03:08:03: 19000000 INFO @ Thu, 09 Dec 2021 03:08:08: 11000000 INFO @ Thu, 09 Dec 2021 03:08:08: 17000000 INFO @ Thu, 09 Dec 2021 03:08:11: 20000000 INFO @ Thu, 09 Dec 2021 03:08:14: 18000000 INFO @ Thu, 09 Dec 2021 03:08:15: 12000000 INFO @ Thu, 09 Dec 2021 03:08:18: 21000000 INFO @ Thu, 09 Dec 2021 03:08:21: 19000000 INFO @ Thu, 09 Dec 2021 03:08:22: 13000000 INFO @ Thu, 09 Dec 2021 03:08:26: 22000000 INFO @ Thu, 09 Dec 2021 03:08:27: 20000000 INFO @ Thu, 09 Dec 2021 03:08:29: 14000000 INFO @ Thu, 09 Dec 2021 03:08:33: 23000000 INFO @ Thu, 09 Dec 2021 03:08:34: 21000000 INFO @ Thu, 09 Dec 2021 03:08:36: 15000000 INFO @ Thu, 09 Dec 2021 03:08:40: 22000000 INFO @ Thu, 09 Dec 2021 03:08:41: 24000000 INFO @ Thu, 09 Dec 2021 03:08:43: 16000000 INFO @ Thu, 09 Dec 2021 03:08:47: 23000000 INFO @ Thu, 09 Dec 2021 03:08:48: 25000000 INFO @ Thu, 09 Dec 2021 03:08:50: 17000000 INFO @ Thu, 09 Dec 2021 03:08:53: 24000000 INFO @ Thu, 09 Dec 2021 03:08:55: 26000000 INFO @ Thu, 09 Dec 2021 03:08:57: 18000000 INFO @ Thu, 09 Dec 2021 03:09:00: 25000000 INFO @ Thu, 09 Dec 2021 03:09:02: 27000000 INFO @ Thu, 09 Dec 2021 03:09:04: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:09:06: 26000000 INFO @ Thu, 09 Dec 2021 03:09:09: 28000000 INFO @ Thu, 09 Dec 2021 03:09:12: 20000000 INFO @ Thu, 09 Dec 2021 03:09:13: 27000000 INFO @ Thu, 09 Dec 2021 03:09:16: 29000000 INFO @ Thu, 09 Dec 2021 03:09:19: 21000000 INFO @ Thu, 09 Dec 2021 03:09:19: 28000000 INFO @ Thu, 09 Dec 2021 03:09:23: 30000000 INFO @ Thu, 09 Dec 2021 03:09:26: 29000000 INFO @ Thu, 09 Dec 2021 03:09:26: 22000000 INFO @ Thu, 09 Dec 2021 03:09:31: 31000000 INFO @ Thu, 09 Dec 2021 03:09:32: 30000000 INFO @ Thu, 09 Dec 2021 03:09:34: 23000000 INFO @ Thu, 09 Dec 2021 03:09:38: 32000000 INFO @ Thu, 09 Dec 2021 03:09:39: 31000000 INFO @ Thu, 09 Dec 2021 03:09:41: 24000000 INFO @ Thu, 09 Dec 2021 03:09:45: 33000000 INFO @ Thu, 09 Dec 2021 03:09:45: 32000000 INFO @ Thu, 09 Dec 2021 03:09:48: 25000000 INFO @ Thu, 09 Dec 2021 03:09:52: 33000000 INFO @ Thu, 09 Dec 2021 03:09:52: 34000000 INFO @ Thu, 09 Dec 2021 03:09:56: 26000000 INFO @ Thu, 09 Dec 2021 03:09:58: 34000000 INFO @ Thu, 09 Dec 2021 03:09:59: 35000000 INFO @ Thu, 09 Dec 2021 03:10:03: 27000000 INFO @ Thu, 09 Dec 2021 03:10:05: 35000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:10:06: 36000000 INFO @ Thu, 09 Dec 2021 03:10:10: 28000000 INFO @ Thu, 09 Dec 2021 03:10:11: 36000000 INFO @ Thu, 09 Dec 2021 03:10:13: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:10:13: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:10:13: #1 total tags in treatment: 16184903 INFO @ Thu, 09 Dec 2021 03:10:13: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:10:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:10:13: #1 tags after filtering in treatment: 14448792 INFO @ Thu, 09 Dec 2021 03:10:13: #1 Redundant rate of treatment: 0.11 INFO @ Thu, 09 Dec 2021 03:10:13: #1 finished! INFO @ Thu, 09 Dec 2021 03:10:13: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:10:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:10:14: #2 number of paired peaks: 398 WARNING @ Thu, 09 Dec 2021 03:10:14: Fewer paired peaks (398) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 398 pairs to build model! INFO @ Thu, 09 Dec 2021 03:10:14: start model_add_line... INFO @ Thu, 09 Dec 2021 03:10:14: start X-correlation... INFO @ Thu, 09 Dec 2021 03:10:14: end of X-cor INFO @ Thu, 09 Dec 2021 03:10:14: #2 finished! INFO @ Thu, 09 Dec 2021 03:10:14: #2 predicted fragment length is 140 bps INFO @ Thu, 09 Dec 2021 03:10:14: #2 alternative fragment length(s) may be 4,140 bps INFO @ Thu, 09 Dec 2021 03:10:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8582580/SRX8582580.05_model.r INFO @ Thu, 09 Dec 2021 03:10:14: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:10:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:10:17: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:10:17: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:10:17: #1 total tags in treatment: 16184903 INFO @ Thu, 09 Dec 2021 03:10:17: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:10:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:10:17: 29000000 INFO @ Thu, 09 Dec 2021 03:10:17: #1 tags after filtering in treatment: 14448792 INFO @ Thu, 09 Dec 2021 03:10:17: #1 Redundant rate of treatment: 0.11 INFO @ Thu, 09 Dec 2021 03:10:17: #1 finished! INFO @ Thu, 09 Dec 2021 03:10:17: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:10:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:10:18: #2 number of paired peaks: 398 WARNING @ Thu, 09 Dec 2021 03:10:18: Fewer paired peaks (398) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 398 pairs to build model! INFO @ Thu, 09 Dec 2021 03:10:18: start model_add_line... INFO @ Thu, 09 Dec 2021 03:10:18: start X-correlation... INFO @ Thu, 09 Dec 2021 03:10:18: end of X-cor INFO @ Thu, 09 Dec 2021 03:10:18: #2 finished! INFO @ Thu, 09 Dec 2021 03:10:18: #2 predicted fragment length is 140 bps INFO @ Thu, 09 Dec 2021 03:10:18: #2 alternative fragment length(s) may be 4,140 bps INFO @ Thu, 09 Dec 2021 03:10:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8582580/SRX8582580.10_model.r INFO @ Thu, 09 Dec 2021 03:10:18: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:10:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:10:24: 30000000 INFO @ Thu, 09 Dec 2021 03:10:30: 31000000 INFO @ Thu, 09 Dec 2021 03:10:37: 32000000 INFO @ Thu, 09 Dec 2021 03:10:43: 33000000 INFO @ Thu, 09 Dec 2021 03:10:44: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:10:47: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:10:50: 34000000 INFO @ Thu, 09 Dec 2021 03:10:56: 35000000 INFO @ Thu, 09 Dec 2021 03:10:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8582580/SRX8582580.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:10:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8582580/SRX8582580.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:10:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8582580/SRX8582580.05_summits.bed INFO @ Thu, 09 Dec 2021 03:10:58: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3874 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:11:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8582580/SRX8582580.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:11:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8582580/SRX8582580.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:11:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8582580/SRX8582580.10_summits.bed INFO @ Thu, 09 Dec 2021 03:11:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1999 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:11:02: 36000000 INFO @ Thu, 09 Dec 2021 03:11:08: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:11:08: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:11:08: #1 total tags in treatment: 16184903 INFO @ Thu, 09 Dec 2021 03:11:08: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:11:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:11:08: #1 tags after filtering in treatment: 14448792 INFO @ Thu, 09 Dec 2021 03:11:08: #1 Redundant rate of treatment: 0.11 INFO @ Thu, 09 Dec 2021 03:11:08: #1 finished! INFO @ Thu, 09 Dec 2021 03:11:08: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:11:08: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:11:09: #2 number of paired peaks: 398 WARNING @ Thu, 09 Dec 2021 03:11:09: Fewer paired peaks (398) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 398 pairs to build model! INFO @ Thu, 09 Dec 2021 03:11:09: start model_add_line... INFO @ Thu, 09 Dec 2021 03:11:09: start X-correlation... INFO @ Thu, 09 Dec 2021 03:11:09: end of X-cor INFO @ Thu, 09 Dec 2021 03:11:09: #2 finished! INFO @ Thu, 09 Dec 2021 03:11:09: #2 predicted fragment length is 140 bps INFO @ Thu, 09 Dec 2021 03:11:09: #2 alternative fragment length(s) may be 4,140 bps INFO @ Thu, 09 Dec 2021 03:11:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8582580/SRX8582580.20_model.r INFO @ Thu, 09 Dec 2021 03:11:09: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:11:09: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:11:37: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:11:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8582580/SRX8582580.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:11:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8582580/SRX8582580.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:11:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8582580/SRX8582580.20_summits.bed INFO @ Thu, 09 Dec 2021 03:11:51: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (799 records, 4 fields): 2 millis CompletedMACS2peakCalling