Job ID = 12265337 SRX = SRX4082386 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:15:57 29366005 reads; of these: 29366005 (100.00%) were paired; of these: 1250796 (4.26%) aligned concordantly 0 times 25306650 (86.18%) aligned concordantly exactly 1 time 2808559 (9.56%) aligned concordantly >1 times ---- 1250796 pairs aligned concordantly 0 times; of these: 394299 (31.52%) aligned discordantly 1 time ---- 856497 pairs aligned 0 times concordantly or discordantly; of these: 1712994 mates make up the pairs; of these: 1324905 (77.34%) aligned 0 times 247654 (14.46%) aligned exactly 1 time 140435 (8.20%) aligned >1 times 97.74% overall alignment rate Time searching: 00:15:58 Overall time: 00:15:58 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] 9205866 / 28481173 = 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 07:04:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082386/SRX4082386.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082386/SRX4082386.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082386/SRX4082386.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 07:04:08: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:04:08: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:04:12: 1000000 INFO @ Sat, 03 Apr 2021 07:04:17: 2000000 INFO @ Sat, 03 Apr 2021 07:04:22: 3000000 INFO @ Sat, 03 Apr 2021 07:04:27: 4000000 INFO @ Sat, 03 Apr 2021 07:04:32: 5000000 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 07:04:37: 6000000 INFO @ Sat, 03 Apr 2021 07:04:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082386/SRX4082386.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082386/SRX4082386.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082386/SRX4082386.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 07:04:38: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:04:38: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:04:42: 7000000 INFO @ Sat, 03 Apr 2021 07:04:44: 1000000 INFO @ Sat, 03 Apr 2021 07:04:48: 8000000 INFO @ Sat, 03 Apr 2021 07:04:51: 2000000 INFO @ Sat, 03 Apr 2021 07:04:54: 9000000 INFO @ Sat, 03 Apr 2021 07:04:58: 3000000 INFO @ Sat, 03 Apr 2021 07:05:00: 10000000 INFO @ Sat, 03 Apr 2021 07:05:04: 4000000 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 07:05:06: 11000000 INFO @ Sat, 03 Apr 2021 07:05:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082386/SRX4082386.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082386/SRX4082386.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082386/SRX4082386.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 07:05:08: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:05:08: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:05:11: 5000000 INFO @ Sat, 03 Apr 2021 07:05:12: 12000000 INFO @ Sat, 03 Apr 2021 07:05:15: 1000000 INFO @ Sat, 03 Apr 2021 07:05:18: 6000000 INFO @ Sat, 03 Apr 2021 07:05:18: 13000000 INFO @ Sat, 03 Apr 2021 07:05:22: 2000000 INFO @ Sat, 03 Apr 2021 07:05:24: 7000000 INFO @ Sat, 03 Apr 2021 07:05:24: 14000000 INFO @ Sat, 03 Apr 2021 07:05:28: 3000000 INFO @ Sat, 03 Apr 2021 07:05:31: 15000000 INFO @ Sat, 03 Apr 2021 07:05:31: 8000000 INFO @ Sat, 03 Apr 2021 07:05:35: 4000000 INFO @ Sat, 03 Apr 2021 07:05:37: 16000000 INFO @ Sat, 03 Apr 2021 07:05:37: 9000000 INFO @ Sat, 03 Apr 2021 07:05:42: 5000000 INFO @ Sat, 03 Apr 2021 07:05:43: 17000000 INFO @ Sat, 03 Apr 2021 07:05:44: 10000000 INFO @ Sat, 03 Apr 2021 07:05:49: 6000000 INFO @ Sat, 03 Apr 2021 07:05:49: 18000000 INFO @ Sat, 03 Apr 2021 07:05:50: 11000000 INFO @ Sat, 03 Apr 2021 07:05:55: 19000000 INFO @ Sat, 03 Apr 2021 07:05:55: 7000000 INFO @ Sat, 03 Apr 2021 07:05:57: 12000000 INFO @ Sat, 03 Apr 2021 07:06:01: 20000000 INFO @ Sat, 03 Apr 2021 07:06:02: 8000000 INFO @ Sat, 03 Apr 2021 07:06:03: 13000000 INFO @ Sat, 03 Apr 2021 07:06:07: 21000000 INFO @ Sat, 03 Apr 2021 07:06:08: 9000000 INFO @ Sat, 03 Apr 2021 07:06:10: 14000000 INFO @ Sat, 03 Apr 2021 07:06:13: 22000000 INFO @ Sat, 03 Apr 2021 07:06:15: 10000000 INFO @ Sat, 03 Apr 2021 07:06:17: 15000000 INFO @ Sat, 03 Apr 2021 07:06:19: 23000000 INFO @ Sat, 03 Apr 2021 07:06:22: 11000000 INFO @ Sat, 03 Apr 2021 07:06:24: 16000000 INFO @ Sat, 03 Apr 2021 07:06:25: 24000000 INFO @ Sat, 03 Apr 2021 07:06:29: 12000000 INFO @ Sat, 03 Apr 2021 07:06:30: 17000000 INFO @ Sat, 03 Apr 2021 07:06:31: 25000000 INFO @ Sat, 03 Apr 2021 07:06:36: 13000000 INFO @ Sat, 03 Apr 2021 07:06:37: 18000000 INFO @ Sat, 03 Apr 2021 07:06:37: 26000000 INFO @ Sat, 03 Apr 2021 07:06:43: 27000000 INFO @ Sat, 03 Apr 2021 07:06:43: 14000000 INFO @ Sat, 03 Apr 2021 07:06:43: 19000000 INFO @ Sat, 03 Apr 2021 07:06:49: 28000000 INFO @ Sat, 03 Apr 2021 07:06:50: 20000000 INFO @ Sat, 03 Apr 2021 07:06:50: 15000000 INFO @ Sat, 03 Apr 2021 07:06:55: 29000000 INFO @ Sat, 03 Apr 2021 07:06:56: 21000000 INFO @ Sat, 03 Apr 2021 07:06:57: 16000000 INFO @ Sat, 03 Apr 2021 07:07:01: 30000000 INFO @ Sat, 03 Apr 2021 07:07:03: 22000000 INFO @ Sat, 03 Apr 2021 07:07:04: 17000000 INFO @ Sat, 03 Apr 2021 07:07:07: 31000000 INFO @ Sat, 03 Apr 2021 07:07:09: 23000000 INFO @ Sat, 03 Apr 2021 07:07:11: 18000000 INFO @ Sat, 03 Apr 2021 07:07:13: 32000000 INFO @ Sat, 03 Apr 2021 07:07:16: 24000000 INFO @ Sat, 03 Apr 2021 07:07:17: 19000000 INFO @ Sat, 03 Apr 2021 07:07:19: 33000000 INFO @ Sat, 03 Apr 2021 07:07:23: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:07:24: 20000000 INFO @ Sat, 03 Apr 2021 07:07:24: 34000000 INFO @ Sat, 03 Apr 2021 07:07:29: 26000000 INFO @ Sat, 03 Apr 2021 07:07:30: 21000000 INFO @ Sat, 03 Apr 2021 07:07:30: 35000000 INFO @ Sat, 03 Apr 2021 07:07:35: 27000000 INFO @ Sat, 03 Apr 2021 07:07:36: 36000000 INFO @ Sat, 03 Apr 2021 07:07:37: 22000000 INFO @ Sat, 03 Apr 2021 07:07:42: 28000000 INFO @ Sat, 03 Apr 2021 07:07:42: 37000000 INFO @ Sat, 03 Apr 2021 07:07:43: 23000000 INFO @ Sat, 03 Apr 2021 07:07:48: 38000000 INFO @ Sat, 03 Apr 2021 07:07:49: 29000000 INFO @ Sat, 03 Apr 2021 07:07:50: 24000000 INFO @ Sat, 03 Apr 2021 07:07:54: #1 tag size is determined as 32 bps INFO @ Sat, 03 Apr 2021 07:07:54: #1 tag size = 32 INFO @ Sat, 03 Apr 2021 07:07:54: #1 total tags in treatment: 18919386 INFO @ Sat, 03 Apr 2021 07:07:54: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:07:54: #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 07:07:55: #1 tags after filtering in treatment: 11546383 INFO @ Sat, 03 Apr 2021 07:07:55: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 03 Apr 2021 07:07:55: #1 finished! INFO @ Sat, 03 Apr 2021 07:07:55: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:07:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:07:55: 30000000 INFO @ Sat, 03 Apr 2021 07:07:55: #2 number of paired peaks: 821 WARNING @ Sat, 03 Apr 2021 07:07:55: Fewer paired peaks (821) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 821 pairs to build model! INFO @ Sat, 03 Apr 2021 07:07:55: start model_add_line... INFO @ Sat, 03 Apr 2021 07:07:56: start X-correlation... INFO @ Sat, 03 Apr 2021 07:07:56: end of X-cor INFO @ Sat, 03 Apr 2021 07:07:56: #2 finished! INFO @ Sat, 03 Apr 2021 07:07:56: #2 predicted fragment length is 92 bps INFO @ Sat, 03 Apr 2021 07:07:56: #2 alternative fragment length(s) may be 92 bps INFO @ Sat, 03 Apr 2021 07:07:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082386/SRX4082386.05_model.r INFO @ Sat, 03 Apr 2021 07:07:56: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:07:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:07:56: 25000000 INFO @ Sat, 03 Apr 2021 07:08:01: 31000000 INFO @ Sat, 03 Apr 2021 07:08:02: 26000000 INFO @ Sat, 03 Apr 2021 07:08:08: 32000000 INFO @ Sat, 03 Apr 2021 07:08:08: 27000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:08:14: 33000000 INFO @ Sat, 03 Apr 2021 07:08:15: 28000000 INFO @ Sat, 03 Apr 2021 07:08:20: 34000000 INFO @ Sat, 03 Apr 2021 07:08:21: 29000000 INFO @ Sat, 03 Apr 2021 07:08:23: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:08:27: 35000000 INFO @ Sat, 03 Apr 2021 07:08:27: 30000000 INFO @ Sat, 03 Apr 2021 07:08:33: 36000000 INFO @ Sat, 03 Apr 2021 07:08:33: 31000000 INFO @ Sat, 03 Apr 2021 07:08:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082386/SRX4082386.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:08:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082386/SRX4082386.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:08:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082386/SRX4082386.05_summits.bed INFO @ Sat, 03 Apr 2021 07:08:37: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (11046 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:08:39: 32000000 INFO @ Sat, 03 Apr 2021 07:08:40: 37000000 INFO @ Sat, 03 Apr 2021 07:08:46: 33000000 INFO @ Sat, 03 Apr 2021 07:08:46: 38000000 INFO @ Sat, 03 Apr 2021 07:08:52: 34000000 INFO @ Sat, 03 Apr 2021 07:08:53: #1 tag size is determined as 32 bps INFO @ Sat, 03 Apr 2021 07:08:53: #1 tag size = 32 INFO @ Sat, 03 Apr 2021 07:08:53: #1 total tags in treatment: 18919386 INFO @ Sat, 03 Apr 2021 07:08:53: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:08:53: #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 07:08:53: #1 tags after filtering in treatment: 11546383 INFO @ Sat, 03 Apr 2021 07:08:53: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 03 Apr 2021 07:08:53: #1 finished! INFO @ Sat, 03 Apr 2021 07:08:53: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:08:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:08:54: #2 number of paired peaks: 821 WARNING @ Sat, 03 Apr 2021 07:08:54: Fewer paired peaks (821) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 821 pairs to build model! INFO @ Sat, 03 Apr 2021 07:08:54: start model_add_line... INFO @ Sat, 03 Apr 2021 07:08:54: start X-correlation... INFO @ Sat, 03 Apr 2021 07:08:54: end of X-cor INFO @ Sat, 03 Apr 2021 07:08:54: #2 finished! INFO @ Sat, 03 Apr 2021 07:08:54: #2 predicted fragment length is 92 bps INFO @ Sat, 03 Apr 2021 07:08:54: #2 alternative fragment length(s) may be 92 bps INFO @ Sat, 03 Apr 2021 07:08:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082386/SRX4082386.10_model.r INFO @ Sat, 03 Apr 2021 07:08:54: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:08:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:08:58: 35000000 INFO @ Sat, 03 Apr 2021 07:09:04: 36000000 INFO @ Sat, 03 Apr 2021 07:09:09: 37000000 INFO @ Sat, 03 Apr 2021 07:09:15: 38000000 INFO @ Sat, 03 Apr 2021 07:09:21: #1 tag size is determined as 32 bps INFO @ Sat, 03 Apr 2021 07:09:21: #1 tag size = 32 INFO @ Sat, 03 Apr 2021 07:09:21: #1 total tags in treatment: 18919386 INFO @ Sat, 03 Apr 2021 07:09:21: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:09:21: #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 07:09:21: #1 tags after filtering in treatment: 11546383 INFO @ Sat, 03 Apr 2021 07:09:21: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 03 Apr 2021 07:09:21: #1 finished! INFO @ Sat, 03 Apr 2021 07:09:21: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:09:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:09:22: #2 number of paired peaks: 821 WARNING @ Sat, 03 Apr 2021 07:09:22: Fewer paired peaks (821) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 821 pairs to build model! INFO @ Sat, 03 Apr 2021 07:09:22: start model_add_line... INFO @ Sat, 03 Apr 2021 07:09:22: start X-correlation... INFO @ Sat, 03 Apr 2021 07:09:22: end of X-cor INFO @ Sat, 03 Apr 2021 07:09:22: #2 finished! INFO @ Sat, 03 Apr 2021 07:09:22: #2 predicted fragment length is 92 bps INFO @ Sat, 03 Apr 2021 07:09:22: #2 alternative fragment length(s) may be 92 bps INFO @ Sat, 03 Apr 2021 07:09:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082386/SRX4082386.20_model.r INFO @ Sat, 03 Apr 2021 07:09:22: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:09:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:09:23: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:09:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082386/SRX4082386.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:09:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082386/SRX4082386.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:09:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082386/SRX4082386.10_summits.bed INFO @ Sat, 03 Apr 2021 07:09:38: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6879 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:09:50: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:10:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082386/SRX4082386.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:10:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082386/SRX4082386.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:10:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082386/SRX4082386.20_summits.bed INFO @ Sat, 03 Apr 2021 07:10:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3581 records, 4 fields): 5 millis CompletedMACS2peakCalling