Job ID = 12264780 SRX = SRX4082386 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 29366005 spots for SRR7164204/SRR7164204.sra Written 29366005 spots for SRR7164204/SRR7164204.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265337 ("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: 00:20:11 29366005 reads; of these: 29366005 (100.00%) were paired; of these: 1252172 (4.26%) aligned concordantly 0 times 25305471 (86.17%) aligned concordantly exactly 1 time 2808362 (9.56%) aligned concordantly >1 times ---- 1252172 pairs aligned concordantly 0 times; of these: 394055 (31.47%) aligned discordantly 1 time ---- 858117 pairs aligned 0 times concordantly or discordantly; of these: 1716234 mates make up the pairs; of these: 1327822 (77.37%) aligned 0 times 247865 (14.44%) aligned exactly 1 time 140547 (8.19%) aligned >1 times 97.74% overall alignment rate Time searching: 00:20:11 Overall time: 00:20:11 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 16 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] 9205515 / 28479586 = 0.3232 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:32:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4082386/SRX4082386.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4082386/SRX4082386.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4082386/SRX4082386.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4082386/SRX4082386.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 @ Sat, 03 Apr 2021 06:32:52: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:32:52: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:32:58: 1000000 INFO @ Sat, 03 Apr 2021 06:33:04: 2000000 INFO @ Sat, 03 Apr 2021 06:33:10: 3000000 INFO @ Sat, 03 Apr 2021 06:33:17: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:33:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4082386/SRX4082386.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4082386/SRX4082386.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4082386/SRX4082386.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4082386/SRX4082386.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 @ Sat, 03 Apr 2021 06:33:22: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:33:22: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:33:24: 5000000 INFO @ Sat, 03 Apr 2021 06:33:29: 1000000 INFO @ Sat, 03 Apr 2021 06:33:31: 6000000 INFO @ Sat, 03 Apr 2021 06:33:38: 2000000 INFO @ Sat, 03 Apr 2021 06:33:39: 7000000 INFO @ Sat, 03 Apr 2021 06:33:46: 3000000 INFO @ Sat, 03 Apr 2021 06:33:47: 8000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:33:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4082386/SRX4082386.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4082386/SRX4082386.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4082386/SRX4082386.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4082386/SRX4082386.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 @ Sat, 03 Apr 2021 06:33:52: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:33:52: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:33:54: 4000000 INFO @ Sat, 03 Apr 2021 06:33:55: 9000000 INFO @ Sat, 03 Apr 2021 06:34:01: 1000000 INFO @ Sat, 03 Apr 2021 06:34:03: 10000000 INFO @ Sat, 03 Apr 2021 06:34:03: 5000000 INFO @ Sat, 03 Apr 2021 06:34:10: 2000000 INFO @ Sat, 03 Apr 2021 06:34:11: 11000000 INFO @ Sat, 03 Apr 2021 06:34:12: 6000000 INFO @ Sat, 03 Apr 2021 06:34:18: 3000000 INFO @ Sat, 03 Apr 2021 06:34:19: 12000000 INFO @ Sat, 03 Apr 2021 06:34:21: 7000000 INFO @ Sat, 03 Apr 2021 06:34:27: 13000000 INFO @ Sat, 03 Apr 2021 06:34:27: 4000000 INFO @ Sat, 03 Apr 2021 06:34:30: 8000000 INFO @ Sat, 03 Apr 2021 06:34:34: 14000000 INFO @ Sat, 03 Apr 2021 06:34:35: 5000000 INFO @ Sat, 03 Apr 2021 06:34:38: 9000000 INFO @ Sat, 03 Apr 2021 06:34:42: 15000000 INFO @ Sat, 03 Apr 2021 06:34:43: 6000000 INFO @ Sat, 03 Apr 2021 06:34:46: 10000000 INFO @ Sat, 03 Apr 2021 06:34:50: 16000000 INFO @ Sat, 03 Apr 2021 06:34:52: 7000000 INFO @ Sat, 03 Apr 2021 06:34:55: 11000000 INFO @ Sat, 03 Apr 2021 06:34:57: 17000000 INFO @ Sat, 03 Apr 2021 06:35:01: 8000000 INFO @ Sat, 03 Apr 2021 06:35:03: 12000000 INFO @ Sat, 03 Apr 2021 06:35:05: 18000000 INFO @ Sat, 03 Apr 2021 06:35:09: 9000000 INFO @ Sat, 03 Apr 2021 06:35:11: 13000000 INFO @ Sat, 03 Apr 2021 06:35:12: 19000000 INFO @ Sat, 03 Apr 2021 06:35:17: 10000000 INFO @ Sat, 03 Apr 2021 06:35:19: 14000000 INFO @ Sat, 03 Apr 2021 06:35:20: 20000000 INFO @ Sat, 03 Apr 2021 06:35:26: 11000000 INFO @ Sat, 03 Apr 2021 06:35:27: 15000000 INFO @ Sat, 03 Apr 2021 06:35:28: 21000000 INFO @ Sat, 03 Apr 2021 06:35:34: 12000000 INFO @ Sat, 03 Apr 2021 06:35:35: 16000000 INFO @ Sat, 03 Apr 2021 06:35:36: 22000000 INFO @ Sat, 03 Apr 2021 06:35:43: 23000000 INFO @ Sat, 03 Apr 2021 06:35:43: 17000000 INFO @ Sat, 03 Apr 2021 06:35:44: 13000000 INFO @ Sat, 03 Apr 2021 06:35:51: 14000000 INFO @ Sat, 03 Apr 2021 06:35:51: 18000000 INFO @ Sat, 03 Apr 2021 06:35:52: 24000000 INFO @ Sat, 03 Apr 2021 06:35:59: 15000000 INFO @ Sat, 03 Apr 2021 06:35:59: 25000000 INFO @ Sat, 03 Apr 2021 06:36:01: 19000000 INFO @ Sat, 03 Apr 2021 06:36:07: 26000000 INFO @ Sat, 03 Apr 2021 06:36:08: 16000000 INFO @ Sat, 03 Apr 2021 06:36:10: 20000000 INFO @ Sat, 03 Apr 2021 06:36:15: 27000000 INFO @ Sat, 03 Apr 2021 06:36:16: 17000000 INFO @ Sat, 03 Apr 2021 06:36:19: 21000000 INFO @ Sat, 03 Apr 2021 06:36:23: 28000000 INFO @ Sat, 03 Apr 2021 06:36:25: 18000000 INFO @ Sat, 03 Apr 2021 06:36:27: 22000000 INFO @ Sat, 03 Apr 2021 06:36:31: 29000000 INFO @ Sat, 03 Apr 2021 06:36:32: 19000000 INFO @ Sat, 03 Apr 2021 06:36:35: 23000000 INFO @ Sat, 03 Apr 2021 06:36:38: 30000000 INFO @ Sat, 03 Apr 2021 06:36:40: 20000000 INFO @ Sat, 03 Apr 2021 06:36:43: 24000000 INFO @ Sat, 03 Apr 2021 06:36:46: 31000000 INFO @ Sat, 03 Apr 2021 06:36:48: 21000000 INFO @ Sat, 03 Apr 2021 06:36:51: 25000000 INFO @ Sat, 03 Apr 2021 06:36:54: 32000000 INFO @ Sat, 03 Apr 2021 06:36:56: 22000000 INFO @ Sat, 03 Apr 2021 06:36:59: 26000000 INFO @ Sat, 03 Apr 2021 06:37:02: 33000000 INFO @ Sat, 03 Apr 2021 06:37:04: 23000000 INFO @ Sat, 03 Apr 2021 06:37:07: 27000000 INFO @ Sat, 03 Apr 2021 06:37:10: 34000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:37:13: 24000000 INFO @ Sat, 03 Apr 2021 06:37:14: 28000000 INFO @ Sat, 03 Apr 2021 06:37:18: 35000000 INFO @ Sat, 03 Apr 2021 06:37:20: 25000000 INFO @ Sat, 03 Apr 2021 06:37:22: 29000000 INFO @ Sat, 03 Apr 2021 06:37:26: 36000000 INFO @ Sat, 03 Apr 2021 06:37:28: 26000000 INFO @ Sat, 03 Apr 2021 06:37:30: 30000000 INFO @ Sat, 03 Apr 2021 06:37:35: 37000000 INFO @ Sat, 03 Apr 2021 06:37:35: 27000000 INFO @ Sat, 03 Apr 2021 06:37:38: 31000000 INFO @ Sat, 03 Apr 2021 06:37:42: 28000000 INFO @ Sat, 03 Apr 2021 06:37:43: 38000000 INFO @ Sat, 03 Apr 2021 06:37:45: 32000000 INFO @ Sat, 03 Apr 2021 06:37:50: 29000000 INFO @ Sat, 03 Apr 2021 06:37:50: #1 tag size is determined as 32 bps INFO @ Sat, 03 Apr 2021 06:37:50: #1 tag size = 32 INFO @ Sat, 03 Apr 2021 06:37:50: #1 total tags in treatment: 18918357 INFO @ Sat, 03 Apr 2021 06:37:50: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:37:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:37:51: #1 tags after filtering in treatment: 11546072 INFO @ Sat, 03 Apr 2021 06:37:51: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 03 Apr 2021 06:37:51: #1 finished! INFO @ Sat, 03 Apr 2021 06:37:51: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:37:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:37:52: #2 number of paired peaks: 820 WARNING @ Sat, 03 Apr 2021 06:37:52: Fewer paired peaks (820) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 820 pairs to build model! INFO @ Sat, 03 Apr 2021 06:37:52: start model_add_line... INFO @ Sat, 03 Apr 2021 06:37:52: start X-correlation... INFO @ Sat, 03 Apr 2021 06:37:52: end of X-cor INFO @ Sat, 03 Apr 2021 06:37:52: #2 finished! INFO @ Sat, 03 Apr 2021 06:37:52: #2 predicted fragment length is 92 bps INFO @ Sat, 03 Apr 2021 06:37:52: #2 alternative fragment length(s) may be 92 bps INFO @ Sat, 03 Apr 2021 06:37:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4082386/SRX4082386.05_model.r INFO @ Sat, 03 Apr 2021 06:37:52: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:37:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:37:53: 33000000 INFO @ Sat, 03 Apr 2021 06:37:56: 30000000 INFO @ Sat, 03 Apr 2021 06:38:00: 34000000 INFO @ Sat, 03 Apr 2021 06:38:03: 31000000 INFO @ Sat, 03 Apr 2021 06:38:07: 35000000 INFO @ Sat, 03 Apr 2021 06:38:10: 32000000 INFO @ Sat, 03 Apr 2021 06:38:14: 36000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:38:17: 33000000 INFO @ Sat, 03 Apr 2021 06:38:17: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:38:21: 37000000 INFO @ Sat, 03 Apr 2021 06:38:25: 34000000 INFO @ Sat, 03 Apr 2021 06:38:30: 38000000 INFO @ Sat, 03 Apr 2021 06:38:31: 35000000 INFO @ Sat, 03 Apr 2021 06:38:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4082386/SRX4082386.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:38:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4082386/SRX4082386.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:38:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4082386/SRX4082386.05_summits.bed INFO @ Sat, 03 Apr 2021 06:38:32: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (11046 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:38:36: #1 tag size is determined as 32 bps INFO @ Sat, 03 Apr 2021 06:38:36: #1 tag size = 32 INFO @ Sat, 03 Apr 2021 06:38:36: #1 total tags in treatment: 18918357 INFO @ Sat, 03 Apr 2021 06:38:36: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:38:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:38:37: #1 tags after filtering in treatment: 11546072 INFO @ Sat, 03 Apr 2021 06:38:37: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 03 Apr 2021 06:38:37: #1 finished! INFO @ Sat, 03 Apr 2021 06:38:37: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:38:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:38:38: 36000000 INFO @ Sat, 03 Apr 2021 06:38:38: #2 number of paired peaks: 820 WARNING @ Sat, 03 Apr 2021 06:38:38: Fewer paired peaks (820) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 820 pairs to build model! INFO @ Sat, 03 Apr 2021 06:38:38: start model_add_line... INFO @ Sat, 03 Apr 2021 06:38:38: start X-correlation... INFO @ Sat, 03 Apr 2021 06:38:38: end of X-cor INFO @ Sat, 03 Apr 2021 06:38:38: #2 finished! INFO @ Sat, 03 Apr 2021 06:38:38: #2 predicted fragment length is 92 bps INFO @ Sat, 03 Apr 2021 06:38:38: #2 alternative fragment length(s) may be 92 bps INFO @ Sat, 03 Apr 2021 06:38:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4082386/SRX4082386.10_model.r INFO @ Sat, 03 Apr 2021 06:38:38: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:38:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:38:44: 37000000 INFO @ Sat, 03 Apr 2021 06:38:49: 38000000 INFO @ Sat, 03 Apr 2021 06:38:55: #1 tag size is determined as 32 bps INFO @ Sat, 03 Apr 2021 06:38:55: #1 tag size = 32 INFO @ Sat, 03 Apr 2021 06:38:55: #1 total tags in treatment: 18918357 INFO @ Sat, 03 Apr 2021 06:38:55: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:38:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:38:55: #1 tags after filtering in treatment: 11546072 INFO @ Sat, 03 Apr 2021 06:38:55: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 03 Apr 2021 06:38:55: #1 finished! INFO @ Sat, 03 Apr 2021 06:38:55: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:38:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:38:56: #2 number of paired peaks: 820 WARNING @ Sat, 03 Apr 2021 06:38:56: Fewer paired peaks (820) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 820 pairs to build model! INFO @ Sat, 03 Apr 2021 06:38:56: start model_add_line... INFO @ Sat, 03 Apr 2021 06:38:56: start X-correlation... INFO @ Sat, 03 Apr 2021 06:38:56: end of X-cor INFO @ Sat, 03 Apr 2021 06:38:56: #2 finished! INFO @ Sat, 03 Apr 2021 06:38:56: #2 predicted fragment length is 92 bps INFO @ Sat, 03 Apr 2021 06:38:56: #2 alternative fragment length(s) may be 92 bps INFO @ Sat, 03 Apr 2021 06:38:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4082386/SRX4082386.20_model.r INFO @ Sat, 03 Apr 2021 06:38:56: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:38:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:39:01: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:39:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4082386/SRX4082386.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:39:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4082386/SRX4082386.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:39:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4082386/SRX4082386.10_summits.bed INFO @ Sat, 03 Apr 2021 06:39:13: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6880 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:39:19: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:39:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4082386/SRX4082386.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:39:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4082386/SRX4082386.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:39:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4082386/SRX4082386.20_summits.bed INFO @ Sat, 03 Apr 2021 06:39:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3581 records, 4 fields): 6 millis CompletedMACS2peakCalling