Job ID = 14158331 SRX = SRX10342596 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10819747 spots for SRR13964648/SRR13964648.sra Written 10819747 spots for SRR13964648/SRR13964648.sra Read 12111971 spots for SRR13964649/SRR13964649.sra Written 12111971 spots for SRR13964649/SRR13964649.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158909 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:15:24 22931718 reads; of these: 22931718 (100.00%) were paired; of these: 2623309 (11.44%) aligned concordantly 0 times 17963838 (78.34%) aligned concordantly exactly 1 time 2344571 (10.22%) aligned concordantly >1 times ---- 2623309 pairs aligned concordantly 0 times; of these: 1661167 (63.32%) aligned discordantly 1 time ---- 962142 pairs aligned 0 times concordantly or discordantly; of these: 1924284 mates make up the pairs; of these: 1213072 (63.04%) aligned 0 times 307885 (16.00%) aligned exactly 1 time 403327 (20.96%) aligned >1 times 97.36% overall alignment rate Time searching: 00:15:25 Overall time: 00:15:25 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] 1779925 / 21946320 = 0.0811 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 16:36:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342596/SRX10342596.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342596/SRX10342596.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342596/SRX10342596.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342596/SRX10342596.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 16:36:52: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:36:52: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:36:56: 1000000 INFO @ Wed, 08 Dec 2021 16:37:00: 2000000 INFO @ Wed, 08 Dec 2021 16:37:03: 3000000 INFO @ Wed, 08 Dec 2021 16:37:07: 4000000 INFO @ Wed, 08 Dec 2021 16:37:11: 5000000 INFO @ Wed, 08 Dec 2021 16:37:15: 6000000 INFO @ Wed, 08 Dec 2021 16:37:19: 7000000 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 16:37:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342596/SRX10342596.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342596/SRX10342596.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342596/SRX10342596.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342596/SRX10342596.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 16:37:22: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:37:22: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:37:23: 8000000 INFO @ Wed, 08 Dec 2021 16:37:26: 1000000 INFO @ Wed, 08 Dec 2021 16:37:27: 9000000 INFO @ Wed, 08 Dec 2021 16:37:30: 2000000 INFO @ Wed, 08 Dec 2021 16:37:31: 10000000 INFO @ Wed, 08 Dec 2021 16:37:34: 3000000 INFO @ Wed, 08 Dec 2021 16:37:35: 11000000 INFO @ Wed, 08 Dec 2021 16:37:38: 4000000 INFO @ Wed, 08 Dec 2021 16:37:39: 12000000 INFO @ Wed, 08 Dec 2021 16:37:42: 5000000 INFO @ Wed, 08 Dec 2021 16:37:42: 13000000 INFO @ Wed, 08 Dec 2021 16:37:46: 6000000 INFO @ Wed, 08 Dec 2021 16:37:46: 14000000 INFO @ Wed, 08 Dec 2021 16:37:50: 7000000 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 16:37:50: 15000000 INFO @ Wed, 08 Dec 2021 16:37:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342596/SRX10342596.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342596/SRX10342596.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342596/SRX10342596.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342596/SRX10342596.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 16:37:52: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:37:52: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:37:54: 8000000 INFO @ Wed, 08 Dec 2021 16:37:54: 16000000 INFO @ Wed, 08 Dec 2021 16:37:56: 1000000 INFO @ Wed, 08 Dec 2021 16:37:58: 9000000 INFO @ Wed, 08 Dec 2021 16:37:58: 17000000 INFO @ Wed, 08 Dec 2021 16:38:01: 2000000 INFO @ Wed, 08 Dec 2021 16:38:02: 10000000 INFO @ Wed, 08 Dec 2021 16:38:03: 18000000 INFO @ Wed, 08 Dec 2021 16:38:05: 3000000 INFO @ Wed, 08 Dec 2021 16:38:06: 11000000 INFO @ Wed, 08 Dec 2021 16:38:07: 19000000 INFO @ Wed, 08 Dec 2021 16:38:10: 12000000 INFO @ Wed, 08 Dec 2021 16:38:10: 4000000 INFO @ Wed, 08 Dec 2021 16:38:11: 20000000 INFO @ Wed, 08 Dec 2021 16:38:14: 13000000 INFO @ Wed, 08 Dec 2021 16:38:14: 5000000 INFO @ Wed, 08 Dec 2021 16:38:15: 21000000 INFO @ Wed, 08 Dec 2021 16:38:18: 14000000 INFO @ Wed, 08 Dec 2021 16:38:19: 22000000 INFO @ Wed, 08 Dec 2021 16:38:19: 6000000 INFO @ Wed, 08 Dec 2021 16:38:22: 15000000 INFO @ Wed, 08 Dec 2021 16:38:23: 23000000 INFO @ Wed, 08 Dec 2021 16:38:23: 7000000 INFO @ Wed, 08 Dec 2021 16:38:26: 16000000 INFO @ Wed, 08 Dec 2021 16:38:27: 24000000 INFO @ Wed, 08 Dec 2021 16:38:28: 8000000 INFO @ Wed, 08 Dec 2021 16:38:30: 17000000 INFO @ Wed, 08 Dec 2021 16:38:31: 25000000 INFO @ Wed, 08 Dec 2021 16:38:33: 9000000 INFO @ Wed, 08 Dec 2021 16:38:34: 18000000 INFO @ Wed, 08 Dec 2021 16:38:35: 26000000 INFO @ Wed, 08 Dec 2021 16:38:37: 10000000 INFO @ Wed, 08 Dec 2021 16:38:38: 19000000 INFO @ Wed, 08 Dec 2021 16:38:39: 27000000 INFO @ Wed, 08 Dec 2021 16:38:42: 11000000 INFO @ Wed, 08 Dec 2021 16:38:43: 20000000 INFO @ Wed, 08 Dec 2021 16:38:43: 28000000 INFO @ Wed, 08 Dec 2021 16:38:47: 12000000 INFO @ Wed, 08 Dec 2021 16:38:47: 21000000 INFO @ Wed, 08 Dec 2021 16:38:47: 29000000 INFO @ Wed, 08 Dec 2021 16:38:51: 22000000 INFO @ Wed, 08 Dec 2021 16:38:51: 13000000 INFO @ Wed, 08 Dec 2021 16:38:51: 30000000 INFO @ Wed, 08 Dec 2021 16:38:55: 23000000 INFO @ Wed, 08 Dec 2021 16:38:55: 31000000 INFO @ Wed, 08 Dec 2021 16:38:56: 14000000 INFO @ Wed, 08 Dec 2021 16:38:59: 24000000 INFO @ Wed, 08 Dec 2021 16:38:59: 32000000 INFO @ Wed, 08 Dec 2021 16:39:00: 15000000 INFO @ Wed, 08 Dec 2021 16:39:03: 25000000 INFO @ Wed, 08 Dec 2021 16:39:04: 33000000 INFO @ Wed, 08 Dec 2021 16:39:05: 16000000 INFO @ Wed, 08 Dec 2021 16:39:07: 26000000 INFO @ Wed, 08 Dec 2021 16:39:08: 34000000 INFO @ Wed, 08 Dec 2021 16:39:10: 17000000 INFO @ Wed, 08 Dec 2021 16:39:11: 27000000 INFO @ Wed, 08 Dec 2021 16:39:12: 35000000 INFO @ Wed, 08 Dec 2021 16:39:14: 18000000 INFO @ Wed, 08 Dec 2021 16:39:15: 28000000 INFO @ Wed, 08 Dec 2021 16:39:16: 36000000 INFO @ Wed, 08 Dec 2021 16:39:19: 19000000 INFO @ Wed, 08 Dec 2021 16:39:19: 29000000 INFO @ Wed, 08 Dec 2021 16:39:20: 37000000 INFO @ Wed, 08 Dec 2021 16:39:23: 30000000 INFO @ Wed, 08 Dec 2021 16:39:24: 20000000 INFO @ Wed, 08 Dec 2021 16:39:24: 38000000 INFO @ Wed, 08 Dec 2021 16:39:27: 31000000 INFO @ Wed, 08 Dec 2021 16:39:28: 39000000 INFO @ Wed, 08 Dec 2021 16:39:28: 21000000 INFO @ Wed, 08 Dec 2021 16:39:31: 32000000 INFO @ Wed, 08 Dec 2021 16:39:32: 40000000 INFO @ Wed, 08 Dec 2021 16:39:33: 22000000 INFO @ Wed, 08 Dec 2021 16:39:35: 33000000 INFO @ Wed, 08 Dec 2021 16:39:36: 41000000 INFO @ Wed, 08 Dec 2021 16:39:36: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 16:39:36: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 16:39:36: #1 total tags in treatment: 18628367 INFO @ Wed, 08 Dec 2021 16:39:36: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:39:36: #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 16:39:37: #1 tags after filtering in treatment: 16958464 INFO @ Wed, 08 Dec 2021 16:39:37: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 08 Dec 2021 16:39:37: #1 finished! INFO @ Wed, 08 Dec 2021 16:39:37: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:39:37: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:39:38: 23000000 INFO @ Wed, 08 Dec 2021 16:39:38: #2 number of paired peaks: 239 WARNING @ Wed, 08 Dec 2021 16:39:38: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Wed, 08 Dec 2021 16:39:38: start model_add_line... INFO @ Wed, 08 Dec 2021 16:39:38: start X-correlation... INFO @ Wed, 08 Dec 2021 16:39:38: end of X-cor INFO @ Wed, 08 Dec 2021 16:39:38: #2 finished! INFO @ Wed, 08 Dec 2021 16:39:38: #2 predicted fragment length is 97 bps INFO @ Wed, 08 Dec 2021 16:39:38: #2 alternative fragment length(s) may be 3,75,97 bps INFO @ Wed, 08 Dec 2021 16:39:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342596/SRX10342596.05_model.r INFO @ Wed, 08 Dec 2021 16:39:38: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:39:38: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:39:40: 34000000 INFO @ Wed, 08 Dec 2021 16:39:42: 24000000 INFO @ Wed, 08 Dec 2021 16:39:44: 35000000 INFO @ Wed, 08 Dec 2021 16:39:47: 25000000 INFO @ Wed, 08 Dec 2021 16:39:48: 36000000 INFO @ Wed, 08 Dec 2021 16:39:52: 26000000 INFO @ Wed, 08 Dec 2021 16:39:52: 37000000 INFO @ Wed, 08 Dec 2021 16:39:56: 38000000 INFO @ Wed, 08 Dec 2021 16:39:56: 27000000 INFO @ Wed, 08 Dec 2021 16:40:00: 39000000 INFO @ Wed, 08 Dec 2021 16:40:01: 28000000 INFO @ Wed, 08 Dec 2021 16:40:04: 40000000 INFO @ Wed, 08 Dec 2021 16:40:05: 29000000 INFO @ Wed, 08 Dec 2021 16:40:08: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:40:08: 41000000 INFO @ Wed, 08 Dec 2021 16:40:09: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 16:40:09: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 16:40:09: #1 total tags in treatment: 18628367 INFO @ Wed, 08 Dec 2021 16:40:09: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:40:09: #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 16:40:09: #1 tags after filtering in treatment: 16958464 INFO @ Wed, 08 Dec 2021 16:40:09: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 08 Dec 2021 16:40:09: #1 finished! INFO @ Wed, 08 Dec 2021 16:40:09: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:40:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:40:10: #2 number of paired peaks: 239 WARNING @ Wed, 08 Dec 2021 16:40:10: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Wed, 08 Dec 2021 16:40:10: start model_add_line... INFO @ Wed, 08 Dec 2021 16:40:10: 30000000 INFO @ Wed, 08 Dec 2021 16:40:10: start X-correlation... INFO @ Wed, 08 Dec 2021 16:40:10: end of X-cor INFO @ Wed, 08 Dec 2021 16:40:10: #2 finished! INFO @ Wed, 08 Dec 2021 16:40:10: #2 predicted fragment length is 97 bps INFO @ Wed, 08 Dec 2021 16:40:10: #2 alternative fragment length(s) may be 3,75,97 bps INFO @ Wed, 08 Dec 2021 16:40:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342596/SRX10342596.10_model.r INFO @ Wed, 08 Dec 2021 16:40:10: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:40:10: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 16:40:15: 31000000 INFO @ Wed, 08 Dec 2021 16:40:19: 32000000 INFO @ Wed, 08 Dec 2021 16:40:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342596/SRX10342596.05_peaks.xls INFO @ Wed, 08 Dec 2021 16:40:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342596/SRX10342596.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:40:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342596/SRX10342596.05_summits.bed INFO @ Wed, 08 Dec 2021 16:40:23: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2578 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 16:40:24: 33000000 INFO @ Wed, 08 Dec 2021 16:40:28: 34000000 INFO @ Wed, 08 Dec 2021 16:40:33: 35000000 INFO @ Wed, 08 Dec 2021 16:40:37: 36000000 INFO @ Wed, 08 Dec 2021 16:40:39: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:40:42: 37000000 INFO @ Wed, 08 Dec 2021 16:40:46: 38000000 INFO @ Wed, 08 Dec 2021 16:40:51: 39000000 INFO @ Wed, 08 Dec 2021 16:40:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342596/SRX10342596.10_peaks.xls INFO @ Wed, 08 Dec 2021 16:40:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342596/SRX10342596.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:40:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342596/SRX10342596.10_summits.bed INFO @ Wed, 08 Dec 2021 16:40:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (601 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 16:40:56: 40000000 INFO @ Wed, 08 Dec 2021 16:41:00: 41000000 INFO @ Wed, 08 Dec 2021 16:41:01: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 16:41:01: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 16:41:01: #1 total tags in treatment: 18628367 INFO @ Wed, 08 Dec 2021 16:41:01: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:41:01: #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 16:41:01: #1 tags after filtering in treatment: 16958464 INFO @ Wed, 08 Dec 2021 16:41:01: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 08 Dec 2021 16:41:01: #1 finished! INFO @ Wed, 08 Dec 2021 16:41:01: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:41:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:41:02: #2 number of paired peaks: 239 WARNING @ Wed, 08 Dec 2021 16:41:02: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Wed, 08 Dec 2021 16:41:02: start model_add_line... INFO @ Wed, 08 Dec 2021 16:41:02: start X-correlation... INFO @ Wed, 08 Dec 2021 16:41:02: end of X-cor INFO @ Wed, 08 Dec 2021 16:41:02: #2 finished! INFO @ Wed, 08 Dec 2021 16:41:02: #2 predicted fragment length is 97 bps INFO @ Wed, 08 Dec 2021 16:41:02: #2 alternative fragment length(s) may be 3,75,97 bps INFO @ Wed, 08 Dec 2021 16:41:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342596/SRX10342596.20_model.r INFO @ Wed, 08 Dec 2021 16:41:02: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:41:02: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 16:41:33: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:41:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342596/SRX10342596.20_peaks.xls INFO @ Wed, 08 Dec 2021 16:41:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342596/SRX10342596.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:41:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342596/SRX10342596.20_summits.bed INFO @ Wed, 08 Dec 2021 16:41:47: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (176 records, 4 fields): 2 millis CompletedMACS2peakCalling