Job ID = 14158183 SRX = SRX10342601 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: 00:19:32 21049530 reads; of these: 21049530 (100.00%) were paired; of these: 5866339 (27.87%) aligned concordantly 0 times 13587053 (64.55%) aligned concordantly exactly 1 time 1596138 (7.58%) aligned concordantly >1 times ---- 5866339 pairs aligned concordantly 0 times; of these: 4315415 (73.56%) aligned discordantly 1 time ---- 1550924 pairs aligned 0 times concordantly or discordantly; of these: 3101848 mates make up the pairs; of these: 1540970 (49.68%) aligned 0 times 634765 (20.46%) aligned exactly 1 time 926113 (29.86%) aligned >1 times 96.34% overall alignment rate Time searching: 00:19:32 Overall time: 00:19:32 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] 3364922 / 19491022 = 0.1726 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 15:06:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342601/SRX10342601.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342601/SRX10342601.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342601/SRX10342601.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342601/SRX10342601.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 15:06:14: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:06:14: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:06:22: 1000000 INFO @ Wed, 08 Dec 2021 15:06:28: 2000000 INFO @ Wed, 08 Dec 2021 15:06:34: 3000000 INFO @ Wed, 08 Dec 2021 15:06:41: 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 15:06:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342601/SRX10342601.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342601/SRX10342601.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342601/SRX10342601.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342601/SRX10342601.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 15:06:44: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:06:44: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:06:48: 5000000 INFO @ Wed, 08 Dec 2021 15:06:53: 1000000 INFO @ Wed, 08 Dec 2021 15:06:55: 6000000 INFO @ Wed, 08 Dec 2021 15:07:01: 2000000 INFO @ Wed, 08 Dec 2021 15:07:03: 7000000 INFO @ Wed, 08 Dec 2021 15:07:09: 3000000 INFO @ Wed, 08 Dec 2021 15:07:11: 8000000 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 15:07:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342601/SRX10342601.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342601/SRX10342601.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342601/SRX10342601.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342601/SRX10342601.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 15:07:14: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:07:14: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:07:17: 4000000 INFO @ Wed, 08 Dec 2021 15:07:19: 9000000 INFO @ Wed, 08 Dec 2021 15:07:22: 1000000 INFO @ Wed, 08 Dec 2021 15:07:25: 5000000 INFO @ Wed, 08 Dec 2021 15:07:28: 10000000 INFO @ Wed, 08 Dec 2021 15:07:30: 2000000 INFO @ Wed, 08 Dec 2021 15:07:33: 6000000 INFO @ Wed, 08 Dec 2021 15:07:36: 11000000 INFO @ Wed, 08 Dec 2021 15:07:37: 3000000 INFO @ Wed, 08 Dec 2021 15:07:41: 7000000 INFO @ Wed, 08 Dec 2021 15:07:44: 12000000 INFO @ Wed, 08 Dec 2021 15:07:44: 4000000 INFO @ Wed, 08 Dec 2021 15:07:49: 8000000 INFO @ Wed, 08 Dec 2021 15:07:51: 5000000 INFO @ Wed, 08 Dec 2021 15:07:52: 13000000 INFO @ Wed, 08 Dec 2021 15:07:57: 9000000 INFO @ Wed, 08 Dec 2021 15:07:59: 6000000 INFO @ Wed, 08 Dec 2021 15:08:00: 14000000 INFO @ Wed, 08 Dec 2021 15:08:05: 10000000 INFO @ Wed, 08 Dec 2021 15:08:06: 7000000 INFO @ Wed, 08 Dec 2021 15:08:08: 15000000 INFO @ Wed, 08 Dec 2021 15:08:13: 11000000 INFO @ Wed, 08 Dec 2021 15:08:14: 8000000 INFO @ Wed, 08 Dec 2021 15:08:17: 16000000 INFO @ Wed, 08 Dec 2021 15:08:22: 9000000 INFO @ Wed, 08 Dec 2021 15:08:22: 12000000 INFO @ Wed, 08 Dec 2021 15:08:25: 17000000 INFO @ Wed, 08 Dec 2021 15:08:29: 10000000 INFO @ Wed, 08 Dec 2021 15:08:31: 13000000 INFO @ Wed, 08 Dec 2021 15:08:33: 18000000 INFO @ Wed, 08 Dec 2021 15:08:36: 11000000 INFO @ Wed, 08 Dec 2021 15:08:40: 14000000 INFO @ Wed, 08 Dec 2021 15:08:41: 19000000 INFO @ Wed, 08 Dec 2021 15:08:44: 12000000 INFO @ Wed, 08 Dec 2021 15:08:49: 15000000 INFO @ Wed, 08 Dec 2021 15:08:49: 20000000 INFO @ Wed, 08 Dec 2021 15:08:51: 13000000 INFO @ Wed, 08 Dec 2021 15:08:56: 16000000 INFO @ Wed, 08 Dec 2021 15:08:58: 21000000 INFO @ Wed, 08 Dec 2021 15:08:58: 14000000 INFO @ Wed, 08 Dec 2021 15:09:04: 17000000 INFO @ Wed, 08 Dec 2021 15:09:06: 15000000 INFO @ Wed, 08 Dec 2021 15:09:06: 22000000 INFO @ Wed, 08 Dec 2021 15:09:13: 18000000 INFO @ Wed, 08 Dec 2021 15:09:13: 16000000 INFO @ Wed, 08 Dec 2021 15:09:14: 23000000 INFO @ Wed, 08 Dec 2021 15:09:21: 17000000 INFO @ Wed, 08 Dec 2021 15:09:22: 19000000 INFO @ Wed, 08 Dec 2021 15:09:22: 24000000 INFO @ Wed, 08 Dec 2021 15:09:28: 18000000 INFO @ Wed, 08 Dec 2021 15:09:30: 25000000 INFO @ Wed, 08 Dec 2021 15:09:30: 20000000 INFO @ Wed, 08 Dec 2021 15:09:36: 19000000 INFO @ Wed, 08 Dec 2021 15:09:38: 26000000 INFO @ Wed, 08 Dec 2021 15:09:38: 21000000 INFO @ Wed, 08 Dec 2021 15:09:43: 20000000 INFO @ Wed, 08 Dec 2021 15:09:45: 27000000 INFO @ Wed, 08 Dec 2021 15:09:46: 22000000 INFO @ Wed, 08 Dec 2021 15:09:51: 21000000 INFO @ Wed, 08 Dec 2021 15:09:53: 28000000 INFO @ Wed, 08 Dec 2021 15:09:54: 23000000 INFO @ Wed, 08 Dec 2021 15:09:58: 22000000 INFO @ Wed, 08 Dec 2021 15:10:01: 29000000 INFO @ Wed, 08 Dec 2021 15:10:03: 24000000 INFO @ Wed, 08 Dec 2021 15:10:06: 23000000 INFO @ Wed, 08 Dec 2021 15:10:09: 30000000 INFO @ Wed, 08 Dec 2021 15:10:12: 25000000 INFO @ Wed, 08 Dec 2021 15:10:13: 24000000 INFO @ Wed, 08 Dec 2021 15:10:16: 31000000 INFO @ Wed, 08 Dec 2021 15:10:20: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 15:10:20: 25000000 INFO @ Wed, 08 Dec 2021 15:10:24: 32000000 INFO @ Wed, 08 Dec 2021 15:10:27: 27000000 INFO @ Wed, 08 Dec 2021 15:10:28: 26000000 INFO @ Wed, 08 Dec 2021 15:10:32: 33000000 INFO @ Wed, 08 Dec 2021 15:10:35: 28000000 INFO @ Wed, 08 Dec 2021 15:10:36: 27000000 INFO @ Wed, 08 Dec 2021 15:10:38: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 15:10:38: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 15:10:38: #1 total tags in treatment: 12377861 INFO @ Wed, 08 Dec 2021 15:10:38: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:10:38: #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 15:10:38: #1 tags after filtering in treatment: 11435126 INFO @ Wed, 08 Dec 2021 15:10:38: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 15:10:38: #1 finished! INFO @ Wed, 08 Dec 2021 15:10:38: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:10:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:10:39: #2 number of paired peaks: 516 WARNING @ Wed, 08 Dec 2021 15:10:39: Fewer paired peaks (516) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 516 pairs to build model! INFO @ Wed, 08 Dec 2021 15:10:39: start model_add_line... INFO @ Wed, 08 Dec 2021 15:10:39: start X-correlation... INFO @ Wed, 08 Dec 2021 15:10:39: end of X-cor INFO @ Wed, 08 Dec 2021 15:10:39: #2 finished! INFO @ Wed, 08 Dec 2021 15:10:39: #2 predicted fragment length is 185 bps INFO @ Wed, 08 Dec 2021 15:10:39: #2 alternative fragment length(s) may be 4,185 bps INFO @ Wed, 08 Dec 2021 15:10:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342601/SRX10342601.05_model.r INFO @ Wed, 08 Dec 2021 15:10:39: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:10:39: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:10:43: 29000000 INFO @ Wed, 08 Dec 2021 15:10:44: 28000000 INFO @ Wed, 08 Dec 2021 15:10:51: 30000000 INFO @ Wed, 08 Dec 2021 15:10:52: 29000000 INFO @ Wed, 08 Dec 2021 15:10:59: 31000000 INFO @ Wed, 08 Dec 2021 15:11:00: 30000000 INFO @ Wed, 08 Dec 2021 15:11:06: 32000000 INFO @ Wed, 08 Dec 2021 15:11:08: 31000000 INFO @ Wed, 08 Dec 2021 15:11:13: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:11:14: 33000000 INFO @ Wed, 08 Dec 2021 15:11:15: 32000000 INFO @ Wed, 08 Dec 2021 15:11:21: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 15:11:21: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 15:11:21: #1 total tags in treatment: 12377861 INFO @ Wed, 08 Dec 2021 15:11:21: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:11:21: #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 15:11:21: #1 tags after filtering in treatment: 11435126 INFO @ Wed, 08 Dec 2021 15:11:21: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 15:11:21: #1 finished! INFO @ Wed, 08 Dec 2021 15:11:21: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:11:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:11:22: #2 number of paired peaks: 516 WARNING @ Wed, 08 Dec 2021 15:11:22: Fewer paired peaks (516) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 516 pairs to build model! INFO @ Wed, 08 Dec 2021 15:11:22: start model_add_line... INFO @ Wed, 08 Dec 2021 15:11:22: start X-correlation... INFO @ Wed, 08 Dec 2021 15:11:22: end of X-cor INFO @ Wed, 08 Dec 2021 15:11:22: #2 finished! INFO @ Wed, 08 Dec 2021 15:11:22: #2 predicted fragment length is 185 bps INFO @ Wed, 08 Dec 2021 15:11:22: #2 alternative fragment length(s) may be 4,185 bps INFO @ Wed, 08 Dec 2021 15:11:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342601/SRX10342601.10_model.r INFO @ Wed, 08 Dec 2021 15:11:22: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:11:22: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:11:23: 33000000 INFO @ Wed, 08 Dec 2021 15:11:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342601/SRX10342601.05_peaks.xls INFO @ Wed, 08 Dec 2021 15:11:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342601/SRX10342601.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:11:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342601/SRX10342601.05_summits.bed INFO @ Wed, 08 Dec 2021 15:11:29: Done! INFO @ Wed, 08 Dec 2021 15:11:29: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 15:11:29: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 15:11:29: #1 total tags in treatment: 12377861 INFO @ Wed, 08 Dec 2021 15:11:29: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:11:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (4982 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 15:11:29: #1 tags after filtering in treatment: 11435126 INFO @ Wed, 08 Dec 2021 15:11:29: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 15:11:29: #1 finished! INFO @ Wed, 08 Dec 2021 15:11:29: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:11:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:11:31: #2 number of paired peaks: 516 WARNING @ Wed, 08 Dec 2021 15:11:31: Fewer paired peaks (516) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 516 pairs to build model! INFO @ Wed, 08 Dec 2021 15:11:31: start model_add_line... INFO @ Wed, 08 Dec 2021 15:11:31: start X-correlation... INFO @ Wed, 08 Dec 2021 15:11:31: end of X-cor INFO @ Wed, 08 Dec 2021 15:11:31: #2 finished! INFO @ Wed, 08 Dec 2021 15:11:31: #2 predicted fragment length is 185 bps INFO @ Wed, 08 Dec 2021 15:11:31: #2 alternative fragment length(s) may be 4,185 bps INFO @ Wed, 08 Dec 2021 15:11:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342601/SRX10342601.20_model.r INFO @ Wed, 08 Dec 2021 15:11:31: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:11:31: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 15:11:57: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:12:04: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:12:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342601/SRX10342601.10_peaks.xls INFO @ Wed, 08 Dec 2021 15:12:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342601/SRX10342601.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:12:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342601/SRX10342601.10_summits.bed INFO @ Wed, 08 Dec 2021 15:12:13: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (3463 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 15:12:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342601/SRX10342601.20_peaks.xls INFO @ Wed, 08 Dec 2021 15:12:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342601/SRX10342601.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:12:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342601/SRX10342601.20_summits.bed INFO @ Wed, 08 Dec 2021 15:12:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1094 records, 4 fields): 4 millis CompletedMACS2peakCalling