Job ID = 14158721 SRX = SRX8976705 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13191251 spots for SRR12483309/SRR12483309.sra Written 13191251 spots for SRR12483309/SRR12483309.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159157 ("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: 00:12:41 13191251 reads; of these: 13191251 (100.00%) were paired; of these: 2179010 (16.52%) aligned concordantly 0 times 8739740 (66.25%) aligned concordantly exactly 1 time 2272501 (17.23%) aligned concordantly >1 times ---- 2179010 pairs aligned concordantly 0 times; of these: 1469303 (67.43%) aligned discordantly 1 time ---- 709707 pairs aligned 0 times concordantly or discordantly; of these: 1419414 mates make up the pairs; of these: 456143 (32.14%) aligned 0 times 383003 (26.98%) aligned exactly 1 time 580268 (40.88%) aligned >1 times 98.27% overall alignment rate Time searching: 00:12:41 Overall time: 00:12:41 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] 3401659 / 12474996 = 0.2727 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 18:01:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976705/SRX8976705.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976705/SRX8976705.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976705/SRX8976705.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976705/SRX8976705.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 18:01:46: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:01:46: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:01:53: 1000000 INFO @ Wed, 08 Dec 2021 18:01:59: 2000000 INFO @ Wed, 08 Dec 2021 18:02:06: 3000000 INFO @ Wed, 08 Dec 2021 18:02:12: 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 18:02:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976705/SRX8976705.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976705/SRX8976705.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976705/SRX8976705.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976705/SRX8976705.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 18:02:16: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:02:16: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:02:19: 5000000 INFO @ Wed, 08 Dec 2021 18:02:22: 1000000 INFO @ Wed, 08 Dec 2021 18:02:27: 6000000 INFO @ Wed, 08 Dec 2021 18:02:29: 2000000 INFO @ Wed, 08 Dec 2021 18:02:34: 7000000 INFO @ Wed, 08 Dec 2021 18:02:35: 3000000 INFO @ Wed, 08 Dec 2021 18:02:41: 8000000 INFO @ Wed, 08 Dec 2021 18:02:42: 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 18:02:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976705/SRX8976705.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976705/SRX8976705.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976705/SRX8976705.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976705/SRX8976705.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 18:02:46: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:02:46: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:02:48: 5000000 INFO @ Wed, 08 Dec 2021 18:02:49: 9000000 INFO @ Wed, 08 Dec 2021 18:02:54: 1000000 INFO @ Wed, 08 Dec 2021 18:02:55: 6000000 INFO @ Wed, 08 Dec 2021 18:02:56: 10000000 INFO @ Wed, 08 Dec 2021 18:03:02: 2000000 INFO @ Wed, 08 Dec 2021 18:03:02: 7000000 INFO @ Wed, 08 Dec 2021 18:03:04: 11000000 INFO @ Wed, 08 Dec 2021 18:03:08: 3000000 INFO @ Wed, 08 Dec 2021 18:03:09: 8000000 INFO @ Wed, 08 Dec 2021 18:03:12: 12000000 INFO @ Wed, 08 Dec 2021 18:03:15: 4000000 INFO @ Wed, 08 Dec 2021 18:03:18: 9000000 INFO @ Wed, 08 Dec 2021 18:03:21: 13000000 INFO @ Wed, 08 Dec 2021 18:03:22: 5000000 INFO @ Wed, 08 Dec 2021 18:03:26: 10000000 INFO @ Wed, 08 Dec 2021 18:03:29: 14000000 INFO @ Wed, 08 Dec 2021 18:03:29: 6000000 INFO @ Wed, 08 Dec 2021 18:03:35: 11000000 INFO @ Wed, 08 Dec 2021 18:03:36: 7000000 INFO @ Wed, 08 Dec 2021 18:03:37: 15000000 INFO @ Wed, 08 Dec 2021 18:03:43: 8000000 INFO @ Wed, 08 Dec 2021 18:03:43: 12000000 INFO @ Wed, 08 Dec 2021 18:03:44: 16000000 INFO @ Wed, 08 Dec 2021 18:03:50: 9000000 INFO @ Wed, 08 Dec 2021 18:03:50: 13000000 INFO @ Wed, 08 Dec 2021 18:03:52: 17000000 INFO @ Wed, 08 Dec 2021 18:03:56: 10000000 INFO @ Wed, 08 Dec 2021 18:03:57: 14000000 INFO @ Wed, 08 Dec 2021 18:03:59: 18000000 INFO @ Wed, 08 Dec 2021 18:04:03: 11000000 INFO @ Wed, 08 Dec 2021 18:04:03: 15000000 INFO @ Wed, 08 Dec 2021 18:04:07: 19000000 INFO @ Wed, 08 Dec 2021 18:04:08: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:04:08: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:04:08: #1 total tags in treatment: 7907079 INFO @ Wed, 08 Dec 2021 18:04:08: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:04:08: #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 18:04:08: #1 tags after filtering in treatment: 7064558 INFO @ Wed, 08 Dec 2021 18:04:08: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 08 Dec 2021 18:04:08: #1 finished! INFO @ Wed, 08 Dec 2021 18:04:08: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:04:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:04:08: #2 number of paired peaks: 761 WARNING @ Wed, 08 Dec 2021 18:04:08: Fewer paired peaks (761) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 761 pairs to build model! INFO @ Wed, 08 Dec 2021 18:04:08: start model_add_line... INFO @ Wed, 08 Dec 2021 18:04:08: start X-correlation... INFO @ Wed, 08 Dec 2021 18:04:08: end of X-cor INFO @ Wed, 08 Dec 2021 18:04:08: #2 finished! INFO @ Wed, 08 Dec 2021 18:04:08: #2 predicted fragment length is 160 bps INFO @ Wed, 08 Dec 2021 18:04:08: #2 alternative fragment length(s) may be 4,160 bps INFO @ Wed, 08 Dec 2021 18:04:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976705/SRX8976705.05_model.r INFO @ Wed, 08 Dec 2021 18:04:08: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:04:08: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:04:09: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:04:10: 16000000 INFO @ Wed, 08 Dec 2021 18:04:16: 13000000 INFO @ Wed, 08 Dec 2021 18:04:16: 17000000 INFO @ Wed, 08 Dec 2021 18:04:22: 14000000 INFO @ Wed, 08 Dec 2021 18:04:22: 18000000 INFO @ Wed, 08 Dec 2021 18:04:24: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:04:28: 15000000 INFO @ Wed, 08 Dec 2021 18:04:29: 19000000 INFO @ Wed, 08 Dec 2021 18:04:29: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:04:29: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:04:29: #1 total tags in treatment: 7907079 INFO @ Wed, 08 Dec 2021 18:04:29: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:04:29: #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 18:04:29: #1 tags after filtering in treatment: 7064558 INFO @ Wed, 08 Dec 2021 18:04:29: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 08 Dec 2021 18:04:29: #1 finished! INFO @ Wed, 08 Dec 2021 18:04:29: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:04:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:04:30: #2 number of paired peaks: 761 WARNING @ Wed, 08 Dec 2021 18:04:30: Fewer paired peaks (761) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 761 pairs to build model! INFO @ Wed, 08 Dec 2021 18:04:30: start model_add_line... INFO @ Wed, 08 Dec 2021 18:04:30: start X-correlation... INFO @ Wed, 08 Dec 2021 18:04:30: end of X-cor INFO @ Wed, 08 Dec 2021 18:04:30: #2 finished! INFO @ Wed, 08 Dec 2021 18:04:30: #2 predicted fragment length is 160 bps INFO @ Wed, 08 Dec 2021 18:04:30: #2 alternative fragment length(s) may be 4,160 bps INFO @ Wed, 08 Dec 2021 18:04:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976705/SRX8976705.10_model.r INFO @ Wed, 08 Dec 2021 18:04:30: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:04:30: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:04:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976705/SRX8976705.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:04:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976705/SRX8976705.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:04:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976705/SRX8976705.05_summits.bed INFO @ Wed, 08 Dec 2021 18:04:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (814 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:04:34: 16000000 INFO @ Wed, 08 Dec 2021 18:04:40: 17000000 INFO @ Wed, 08 Dec 2021 18:04:45: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:04:46: 18000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:04:52: 19000000 INFO @ Wed, 08 Dec 2021 18:04:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976705/SRX8976705.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:04:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976705/SRX8976705.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:04:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976705/SRX8976705.10_summits.bed INFO @ Wed, 08 Dec 2021 18:04:52: Done! INFO @ Wed, 08 Dec 2021 18:04:52: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:04:52: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:04:52: #1 total tags in treatment: 7907079 INFO @ Wed, 08 Dec 2021 18:04:52: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:04:52: #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 18:04:52: #1 tags after filtering in treatment: 7064558 INFO @ Wed, 08 Dec 2021 18:04:52: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 08 Dec 2021 18:04:52: #1 finished! INFO @ Wed, 08 Dec 2021 18:04:52: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:04:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:04:53: #2 number of paired peaks: 761 WARNING @ Wed, 08 Dec 2021 18:04:53: Fewer paired peaks (761) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 761 pairs to build model! INFO @ Wed, 08 Dec 2021 18:04:53: start model_add_line... INFO @ Wed, 08 Dec 2021 18:04:53: start X-correlation... INFO @ Wed, 08 Dec 2021 18:04:53: end of X-cor INFO @ Wed, 08 Dec 2021 18:04:53: #2 finished! INFO @ Wed, 08 Dec 2021 18:04:53: #2 predicted fragment length is 160 bps INFO @ Wed, 08 Dec 2021 18:04:53: #2 alternative fragment length(s) may be 4,160 bps INFO @ Wed, 08 Dec 2021 18:04:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976705/SRX8976705.20_model.r INFO @ Wed, 08 Dec 2021 18:04:53: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:04:53: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (451 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:05:09: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:05:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976705/SRX8976705.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:05:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976705/SRX8976705.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:05:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976705/SRX8976705.20_summits.bed INFO @ Wed, 08 Dec 2021 18:05:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (267 records, 4 fields): 1 millis CompletedMACS2peakCalling