Job ID = 14158319 SRX = SRX10342592 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 11711396 spots for SRR13964640/SRR13964640.sra Written 11711396 spots for SRR13964640/SRR13964640.sra Read 12825104 spots for SRR13964641/SRR13964641.sra Written 12825104 spots for SRR13964641/SRR13964641.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158884 ("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: 00:16:38 24536500 reads; of these: 24536500 (100.00%) were paired; of these: 9693186 (39.51%) aligned concordantly 0 times 12908098 (52.61%) aligned concordantly exactly 1 time 1935216 (7.89%) aligned concordantly >1 times ---- 9693186 pairs aligned concordantly 0 times; of these: 6035144 (62.26%) aligned discordantly 1 time ---- 3658042 pairs aligned 0 times concordantly or discordantly; of these: 7316084 mates make up the pairs; of these: 5132965 (70.16%) aligned 0 times 877460 (11.99%) aligned exactly 1 time 1305659 (17.85%) aligned >1 times 89.54% overall alignment rate Time searching: 00:16:38 Overall time: 00:16:38 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] 7421773 / 20870403 = 0.3556 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 16:27:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342592/SRX10342592.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342592/SRX10342592.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342592/SRX10342592.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342592/SRX10342592.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 16:27:51: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:27:51: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:27:56: 1000000 INFO @ Wed, 08 Dec 2021 16:28:01: 2000000 INFO @ Wed, 08 Dec 2021 16:28:07: 3000000 INFO @ Wed, 08 Dec 2021 16:28:12: 4000000 INFO @ Wed, 08 Dec 2021 16:28:18: 5000000 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 16:28:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342592/SRX10342592.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342592/SRX10342592.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342592/SRX10342592.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342592/SRX10342592.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 16:28:20: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:28:20: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:28:24: 6000000 INFO @ Wed, 08 Dec 2021 16:28:26: 1000000 INFO @ Wed, 08 Dec 2021 16:28:30: 7000000 INFO @ Wed, 08 Dec 2021 16:28:31: 2000000 INFO @ Wed, 08 Dec 2021 16:28:36: 8000000 INFO @ Wed, 08 Dec 2021 16:28:37: 3000000 INFO @ Wed, 08 Dec 2021 16:28:42: 9000000 INFO @ Wed, 08 Dec 2021 16:28:42: 4000000 INFO @ Wed, 08 Dec 2021 16:28:48: 5000000 INFO @ Wed, 08 Dec 2021 16:28:48: 10000000 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 16:28:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342592/SRX10342592.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342592/SRX10342592.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342592/SRX10342592.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342592/SRX10342592.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 16:28:50: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:28:50: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:28:53: 6000000 INFO @ Wed, 08 Dec 2021 16:28:54: 11000000 INFO @ Wed, 08 Dec 2021 16:28:57: 1000000 INFO @ Wed, 08 Dec 2021 16:28:59: 7000000 INFO @ Wed, 08 Dec 2021 16:29:00: 12000000 INFO @ Wed, 08 Dec 2021 16:29:03: 2000000 INFO @ Wed, 08 Dec 2021 16:29:05: 8000000 INFO @ Wed, 08 Dec 2021 16:29:06: 13000000 INFO @ Wed, 08 Dec 2021 16:29:09: 3000000 INFO @ Wed, 08 Dec 2021 16:29:11: 9000000 INFO @ Wed, 08 Dec 2021 16:29:12: 14000000 INFO @ Wed, 08 Dec 2021 16:29:16: 4000000 INFO @ Wed, 08 Dec 2021 16:29:16: 10000000 INFO @ Wed, 08 Dec 2021 16:29:18: 15000000 INFO @ Wed, 08 Dec 2021 16:29:22: 11000000 INFO @ Wed, 08 Dec 2021 16:29:22: 5000000 INFO @ Wed, 08 Dec 2021 16:29:24: 16000000 INFO @ Wed, 08 Dec 2021 16:29:28: 12000000 INFO @ Wed, 08 Dec 2021 16:29:29: 6000000 INFO @ Wed, 08 Dec 2021 16:29:30: 17000000 INFO @ Wed, 08 Dec 2021 16:29:33: 13000000 INFO @ Wed, 08 Dec 2021 16:29:35: 7000000 INFO @ Wed, 08 Dec 2021 16:29:36: 18000000 INFO @ Wed, 08 Dec 2021 16:29:39: 14000000 INFO @ Wed, 08 Dec 2021 16:29:41: 8000000 INFO @ Wed, 08 Dec 2021 16:29:42: 19000000 INFO @ Wed, 08 Dec 2021 16:29:45: 15000000 INFO @ Wed, 08 Dec 2021 16:29:47: 9000000 INFO @ Wed, 08 Dec 2021 16:29:48: 20000000 INFO @ Wed, 08 Dec 2021 16:29:50: 16000000 INFO @ Wed, 08 Dec 2021 16:29:53: 10000000 INFO @ Wed, 08 Dec 2021 16:29:54: 21000000 INFO @ Wed, 08 Dec 2021 16:29:56: 17000000 INFO @ Wed, 08 Dec 2021 16:30:00: 11000000 INFO @ Wed, 08 Dec 2021 16:30:00: 22000000 INFO @ Wed, 08 Dec 2021 16:30:02: 18000000 INFO @ Wed, 08 Dec 2021 16:30:06: 12000000 INFO @ Wed, 08 Dec 2021 16:30:06: 23000000 INFO @ Wed, 08 Dec 2021 16:30:07: 19000000 INFO @ Wed, 08 Dec 2021 16:30:12: 13000000 INFO @ Wed, 08 Dec 2021 16:30:12: 24000000 INFO @ Wed, 08 Dec 2021 16:30:13: 20000000 INFO @ Wed, 08 Dec 2021 16:30:18: 25000000 INFO @ Wed, 08 Dec 2021 16:30:18: 14000000 INFO @ Wed, 08 Dec 2021 16:30:19: 21000000 INFO @ Wed, 08 Dec 2021 16:30:24: 26000000 INFO @ Wed, 08 Dec 2021 16:30:24: 15000000 INFO @ Wed, 08 Dec 2021 16:30:24: 22000000 INFO @ Wed, 08 Dec 2021 16:30:30: 27000000 INFO @ Wed, 08 Dec 2021 16:30:30: 23000000 INFO @ Wed, 08 Dec 2021 16:30:30: 16000000 INFO @ Wed, 08 Dec 2021 16:30:35: 24000000 INFO @ Wed, 08 Dec 2021 16:30:36: 28000000 INFO @ Wed, 08 Dec 2021 16:30:36: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 16:30:41: 25000000 INFO @ Wed, 08 Dec 2021 16:30:42: 29000000 INFO @ Wed, 08 Dec 2021 16:30:42: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 16:30:42: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 16:30:42: #1 total tags in treatment: 9162657 INFO @ Wed, 08 Dec 2021 16:30:42: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:30:42: #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 16:30:42: 18000000 INFO @ Wed, 08 Dec 2021 16:30:42: #1 tags after filtering in treatment: 8469672 INFO @ Wed, 08 Dec 2021 16:30:42: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 16:30:42: #1 finished! INFO @ Wed, 08 Dec 2021 16:30:42: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:30:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:30:43: #2 number of paired peaks: 574 WARNING @ Wed, 08 Dec 2021 16:30:43: Fewer paired peaks (574) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 574 pairs to build model! INFO @ Wed, 08 Dec 2021 16:30:43: start model_add_line... INFO @ Wed, 08 Dec 2021 16:30:43: start X-correlation... INFO @ Wed, 08 Dec 2021 16:30:43: end of X-cor INFO @ Wed, 08 Dec 2021 16:30:43: #2 finished! INFO @ Wed, 08 Dec 2021 16:30:43: #2 predicted fragment length is 134 bps INFO @ Wed, 08 Dec 2021 16:30:43: #2 alternative fragment length(s) may be 4,134,154 bps INFO @ Wed, 08 Dec 2021 16:30:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342592/SRX10342592.05_model.r INFO @ Wed, 08 Dec 2021 16:30:43: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:30:43: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:30:46: 26000000 INFO @ Wed, 08 Dec 2021 16:30:48: 19000000 INFO @ Wed, 08 Dec 2021 16:30:52: 27000000 INFO @ Wed, 08 Dec 2021 16:30:54: 20000000 INFO @ Wed, 08 Dec 2021 16:30:57: 28000000 INFO @ Wed, 08 Dec 2021 16:31:00: 21000000 INFO @ Wed, 08 Dec 2021 16:31:00: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:31:03: 29000000 INFO @ Wed, 08 Dec 2021 16:31:03: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 16:31:03: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 16:31:03: #1 total tags in treatment: 9162657 INFO @ Wed, 08 Dec 2021 16:31:03: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:31:03: #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 16:31:03: #1 tags after filtering in treatment: 8469672 INFO @ Wed, 08 Dec 2021 16:31:03: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 16:31:03: #1 finished! INFO @ Wed, 08 Dec 2021 16:31:03: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:31:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:31:04: #2 number of paired peaks: 574 WARNING @ Wed, 08 Dec 2021 16:31:04: Fewer paired peaks (574) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 574 pairs to build model! INFO @ Wed, 08 Dec 2021 16:31:04: start model_add_line... INFO @ Wed, 08 Dec 2021 16:31:04: start X-correlation... INFO @ Wed, 08 Dec 2021 16:31:04: end of X-cor INFO @ Wed, 08 Dec 2021 16:31:04: #2 finished! INFO @ Wed, 08 Dec 2021 16:31:04: #2 predicted fragment length is 134 bps INFO @ Wed, 08 Dec 2021 16:31:04: #2 alternative fragment length(s) may be 4,134,154 bps INFO @ Wed, 08 Dec 2021 16:31:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342592/SRX10342592.10_model.r INFO @ Wed, 08 Dec 2021 16:31:04: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:31:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:31:06: 22000000 INFO @ Wed, 08 Dec 2021 16:31:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342592/SRX10342592.05_peaks.xls INFO @ Wed, 08 Dec 2021 16:31:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342592/SRX10342592.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:31:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342592/SRX10342592.05_summits.bed INFO @ Wed, 08 Dec 2021 16:31:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1847 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 16:31:12: 23000000 INFO @ Wed, 08 Dec 2021 16:31:17: 24000000 INFO @ Wed, 08 Dec 2021 16:31:21: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:31:23: 25000000 INFO @ Wed, 08 Dec 2021 16:31:28: 26000000 INFO @ Wed, 08 Dec 2021 16:31:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342592/SRX10342592.10_peaks.xls INFO @ Wed, 08 Dec 2021 16:31:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342592/SRX10342592.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:31:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342592/SRX10342592.10_summits.bed INFO @ Wed, 08 Dec 2021 16:31:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (482 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 16:31:33: 27000000 INFO @ Wed, 08 Dec 2021 16:31:39: 28000000 INFO @ Wed, 08 Dec 2021 16:31:44: 29000000 INFO @ Wed, 08 Dec 2021 16:31:44: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 16:31:44: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 16:31:44: #1 total tags in treatment: 9162657 INFO @ Wed, 08 Dec 2021 16:31:44: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:31:44: #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 16:31:45: #1 tags after filtering in treatment: 8469672 INFO @ Wed, 08 Dec 2021 16:31:45: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 16:31:45: #1 finished! INFO @ Wed, 08 Dec 2021 16:31:45: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:31:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:31:45: #2 number of paired peaks: 574 WARNING @ Wed, 08 Dec 2021 16:31:45: Fewer paired peaks (574) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 574 pairs to build model! INFO @ Wed, 08 Dec 2021 16:31:45: start model_add_line... INFO @ Wed, 08 Dec 2021 16:31:45: start X-correlation... INFO @ Wed, 08 Dec 2021 16:31:45: end of X-cor INFO @ Wed, 08 Dec 2021 16:31:45: #2 finished! INFO @ Wed, 08 Dec 2021 16:31:45: #2 predicted fragment length is 134 bps INFO @ Wed, 08 Dec 2021 16:31:45: #2 alternative fragment length(s) may be 4,134,154 bps INFO @ Wed, 08 Dec 2021 16:31:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342592/SRX10342592.20_model.r INFO @ Wed, 08 Dec 2021 16:31:45: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:31:45: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:32:02: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:32:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342592/SRX10342592.20_peaks.xls INFO @ Wed, 08 Dec 2021 16:32:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342592/SRX10342592.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:32:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342592/SRX10342592.20_summits.bed INFO @ Wed, 08 Dec 2021 16:32:11: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (230 records, 4 fields): 2 millis CompletedMACS2peakCalling