Job ID = 6367771 SRX = SRX4085341 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:33:05 prefetch.2.10.7: 1) Downloading 'SRR7167370'... 2020-06-15T23:33:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:46:41 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:46:41 prefetch.2.10.7: 1) 'SRR7167370' was downloaded successfully Read 26582614 spots for SRR7167370/SRR7167370.sra Written 26582614 spots for SRR7167370/SRR7167370.sra 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: 00:22:24 26582614 reads; of these: 26582614 (100.00%) were paired; of these: 2078878 (7.82%) aligned concordantly 0 times 21431969 (80.62%) aligned concordantly exactly 1 time 3071767 (11.56%) aligned concordantly >1 times ---- 2078878 pairs aligned concordantly 0 times; of these: 205854 (9.90%) aligned discordantly 1 time ---- 1873024 pairs aligned 0 times concordantly or discordantly; of these: 3746048 mates make up the pairs; of these: 2083347 (55.61%) aligned 0 times 1381681 (36.88%) aligned exactly 1 time 281020 (7.50%) aligned >1 times 96.08% overall alignment rate Time searching: 00:22:24 Overall time: 00:22:24 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 24 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] 6136874 / 24643551 = 0.2490 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:25:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085341/SRX4085341.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085341/SRX4085341.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085341/SRX4085341.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085341/SRX4085341.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 @ Tue, 16 Jun 2020 09:25:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:25:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:25:34: 1000000 INFO @ Tue, 16 Jun 2020 09:25:41: 2000000 INFO @ Tue, 16 Jun 2020 09:25:48: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:25:55: 4000000 INFO @ Tue, 16 Jun 2020 09:25:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085341/SRX4085341.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085341/SRX4085341.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085341/SRX4085341.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085341/SRX4085341.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 @ Tue, 16 Jun 2020 09:25:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:25:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:26:03: 5000000 INFO @ Tue, 16 Jun 2020 09:26:03: 1000000 INFO @ Tue, 16 Jun 2020 09:26:10: 2000000 INFO @ Tue, 16 Jun 2020 09:26:10: 6000000 INFO @ Tue, 16 Jun 2020 09:26:16: 3000000 INFO @ Tue, 16 Jun 2020 09:26:18: 7000000 INFO @ Tue, 16 Jun 2020 09:26:23: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:26:25: 8000000 INFO @ Tue, 16 Jun 2020 09:26:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085341/SRX4085341.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085341/SRX4085341.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085341/SRX4085341.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085341/SRX4085341.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 @ Tue, 16 Jun 2020 09:26:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:26:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:26:29: 5000000 INFO @ Tue, 16 Jun 2020 09:26:33: 9000000 INFO @ Tue, 16 Jun 2020 09:26:34: 1000000 INFO @ Tue, 16 Jun 2020 09:26:36: 6000000 INFO @ Tue, 16 Jun 2020 09:26:40: 10000000 INFO @ Tue, 16 Jun 2020 09:26:41: 2000000 INFO @ Tue, 16 Jun 2020 09:26:42: 7000000 INFO @ Tue, 16 Jun 2020 09:26:48: 11000000 INFO @ Tue, 16 Jun 2020 09:26:48: 3000000 INFO @ Tue, 16 Jun 2020 09:26:49: 8000000 INFO @ Tue, 16 Jun 2020 09:26:55: 9000000 INFO @ Tue, 16 Jun 2020 09:26:55: 12000000 INFO @ Tue, 16 Jun 2020 09:26:55: 4000000 INFO @ Tue, 16 Jun 2020 09:27:01: 10000000 INFO @ Tue, 16 Jun 2020 09:27:03: 5000000 INFO @ Tue, 16 Jun 2020 09:27:03: 13000000 INFO @ Tue, 16 Jun 2020 09:27:08: 11000000 INFO @ Tue, 16 Jun 2020 09:27:10: 6000000 INFO @ Tue, 16 Jun 2020 09:27:10: 14000000 INFO @ Tue, 16 Jun 2020 09:27:14: 12000000 INFO @ Tue, 16 Jun 2020 09:27:17: 7000000 INFO @ Tue, 16 Jun 2020 09:27:18: 15000000 INFO @ Tue, 16 Jun 2020 09:27:21: 13000000 INFO @ Tue, 16 Jun 2020 09:27:24: 8000000 INFO @ Tue, 16 Jun 2020 09:27:25: 16000000 INFO @ Tue, 16 Jun 2020 09:27:27: 14000000 INFO @ Tue, 16 Jun 2020 09:27:31: 9000000 INFO @ Tue, 16 Jun 2020 09:27:33: 17000000 INFO @ Tue, 16 Jun 2020 09:27:33: 15000000 INFO @ Tue, 16 Jun 2020 09:27:39: 10000000 INFO @ Tue, 16 Jun 2020 09:27:40: 16000000 INFO @ Tue, 16 Jun 2020 09:27:40: 18000000 INFO @ Tue, 16 Jun 2020 09:27:46: 11000000 INFO @ Tue, 16 Jun 2020 09:27:46: 17000000 INFO @ Tue, 16 Jun 2020 09:27:47: 19000000 INFO @ Tue, 16 Jun 2020 09:27:52: 18000000 INFO @ Tue, 16 Jun 2020 09:27:54: 12000000 INFO @ Tue, 16 Jun 2020 09:27:55: 20000000 INFO @ Tue, 16 Jun 2020 09:27:59: 19000000 INFO @ Tue, 16 Jun 2020 09:28:01: 13000000 INFO @ Tue, 16 Jun 2020 09:28:03: 21000000 INFO @ Tue, 16 Jun 2020 09:28:05: 20000000 INFO @ Tue, 16 Jun 2020 09:28:09: 14000000 INFO @ Tue, 16 Jun 2020 09:28:10: 22000000 INFO @ Tue, 16 Jun 2020 09:28:12: 21000000 INFO @ Tue, 16 Jun 2020 09:28:16: 15000000 INFO @ Tue, 16 Jun 2020 09:28:18: 23000000 INFO @ Tue, 16 Jun 2020 09:28:18: 22000000 INFO @ Tue, 16 Jun 2020 09:28:24: 16000000 INFO @ Tue, 16 Jun 2020 09:28:25: 23000000 INFO @ Tue, 16 Jun 2020 09:28:26: 24000000 INFO @ Tue, 16 Jun 2020 09:28:31: 17000000 INFO @ Tue, 16 Jun 2020 09:28:31: 24000000 INFO @ Tue, 16 Jun 2020 09:28:34: 25000000 INFO @ Tue, 16 Jun 2020 09:28:38: 25000000 INFO @ Tue, 16 Jun 2020 09:28:38: 18000000 INFO @ Tue, 16 Jun 2020 09:28:42: 26000000 INFO @ Tue, 16 Jun 2020 09:28:44: 26000000 INFO @ Tue, 16 Jun 2020 09:28:46: 19000000 INFO @ Tue, 16 Jun 2020 09:28:50: 27000000 INFO @ Tue, 16 Jun 2020 09:28:50: 27000000 INFO @ Tue, 16 Jun 2020 09:28:53: 20000000 INFO @ Tue, 16 Jun 2020 09:28:58: 28000000 INFO @ Tue, 16 Jun 2020 09:28:58: 28000000 INFO @ Tue, 16 Jun 2020 09:29:01: 21000000 INFO @ Tue, 16 Jun 2020 09:29:06: 29000000 INFO @ Tue, 16 Jun 2020 09:29:06: 29000000 INFO @ Tue, 16 Jun 2020 09:29:08: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:29:14: 30000000 INFO @ Tue, 16 Jun 2020 09:29:15: 30000000 INFO @ Tue, 16 Jun 2020 09:29:16: 23000000 INFO @ Tue, 16 Jun 2020 09:29:21: 31000000 INFO @ Tue, 16 Jun 2020 09:29:22: 31000000 INFO @ Tue, 16 Jun 2020 09:29:23: 24000000 INFO @ Tue, 16 Jun 2020 09:29:28: 32000000 INFO @ Tue, 16 Jun 2020 09:29:30: 32000000 INFO @ Tue, 16 Jun 2020 09:29:31: 25000000 INFO @ Tue, 16 Jun 2020 09:29:34: 33000000 INFO @ Tue, 16 Jun 2020 09:29:38: 33000000 INFO @ Tue, 16 Jun 2020 09:29:39: 26000000 INFO @ Tue, 16 Jun 2020 09:29:41: 34000000 INFO @ Tue, 16 Jun 2020 09:29:45: 34000000 INFO @ Tue, 16 Jun 2020 09:29:46: 27000000 INFO @ Tue, 16 Jun 2020 09:29:47: 35000000 INFO @ Tue, 16 Jun 2020 09:29:52: 35000000 INFO @ Tue, 16 Jun 2020 09:29:54: 28000000 INFO @ Tue, 16 Jun 2020 09:29:54: 36000000 INFO @ Tue, 16 Jun 2020 09:29:59: 36000000 INFO @ Tue, 16 Jun 2020 09:30:00: 37000000 INFO @ Tue, 16 Jun 2020 09:30:01: 29000000 INFO @ Tue, 16 Jun 2020 09:30:06: 37000000 INFO @ Tue, 16 Jun 2020 09:30:07: 38000000 INFO @ Tue, 16 Jun 2020 09:30:09: 30000000 INFO @ Tue, 16 Jun 2020 09:30:12: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:30:12: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:30:12: #1 total tags in treatment: 18387350 INFO @ Tue, 16 Jun 2020 09:30:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:30:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:30:12: #1 tags after filtering in treatment: 15840378 INFO @ Tue, 16 Jun 2020 09:30:12: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 16 Jun 2020 09:30:12: #1 finished! INFO @ Tue, 16 Jun 2020 09:30:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:30:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:30:13: #2 number of paired peaks: 193 WARNING @ Tue, 16 Jun 2020 09:30:13: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Tue, 16 Jun 2020 09:30:13: start model_add_line... INFO @ Tue, 16 Jun 2020 09:30:13: start X-correlation... INFO @ Tue, 16 Jun 2020 09:30:13: end of X-cor INFO @ Tue, 16 Jun 2020 09:30:13: #2 finished! INFO @ Tue, 16 Jun 2020 09:30:13: #2 predicted fragment length is 106 bps INFO @ Tue, 16 Jun 2020 09:30:13: #2 alternative fragment length(s) may be 3,84,106 bps INFO @ Tue, 16 Jun 2020 09:30:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085341/SRX4085341.10_model.r INFO @ Tue, 16 Jun 2020 09:30:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:30:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:30:13: 38000000 INFO @ Tue, 16 Jun 2020 09:30:16: 31000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:30:19: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:30:19: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:30:19: #1 total tags in treatment: 18387350 INFO @ Tue, 16 Jun 2020 09:30:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:30:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:30:19: #1 tags after filtering in treatment: 15840378 INFO @ Tue, 16 Jun 2020 09:30:19: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 16 Jun 2020 09:30:19: #1 finished! INFO @ Tue, 16 Jun 2020 09:30:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:30:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:30:20: #2 number of paired peaks: 193 WARNING @ Tue, 16 Jun 2020 09:30:20: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Tue, 16 Jun 2020 09:30:20: start model_add_line... INFO @ Tue, 16 Jun 2020 09:30:20: start X-correlation... INFO @ Tue, 16 Jun 2020 09:30:20: end of X-cor INFO @ Tue, 16 Jun 2020 09:30:20: #2 finished! INFO @ Tue, 16 Jun 2020 09:30:20: #2 predicted fragment length is 106 bps INFO @ Tue, 16 Jun 2020 09:30:20: #2 alternative fragment length(s) may be 3,84,106 bps INFO @ Tue, 16 Jun 2020 09:30:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085341/SRX4085341.05_model.r INFO @ Tue, 16 Jun 2020 09:30:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:30:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:30:23: 32000000 INFO @ Tue, 16 Jun 2020 09:30:30: 33000000 INFO @ Tue, 16 Jun 2020 09:30:37: 34000000 INFO @ Tue, 16 Jun 2020 09:30:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:30:44: 35000000 INFO @ Tue, 16 Jun 2020 09:30:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:30:51: 36000000 INFO @ Tue, 16 Jun 2020 09:30:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085341/SRX4085341.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:30:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085341/SRX4085341.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:30:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085341/SRX4085341.10_summits.bed INFO @ Tue, 16 Jun 2020 09:30:57: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (714 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:30:58: 37000000 INFO @ Tue, 16 Jun 2020 09:31:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085341/SRX4085341.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:31:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085341/SRX4085341.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:31:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085341/SRX4085341.05_summits.bed INFO @ Tue, 16 Jun 2020 09:31:05: Done! INFO @ Tue, 16 Jun 2020 09:31:05: 38000000 pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1106 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:31:10: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:31:10: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:31:10: #1 total tags in treatment: 18387350 INFO @ Tue, 16 Jun 2020 09:31:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:31:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:31:10: #1 tags after filtering in treatment: 15840378 INFO @ Tue, 16 Jun 2020 09:31:10: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 16 Jun 2020 09:31:10: #1 finished! INFO @ Tue, 16 Jun 2020 09:31:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:31:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:31:12: #2 number of paired peaks: 193 WARNING @ Tue, 16 Jun 2020 09:31:12: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Tue, 16 Jun 2020 09:31:12: start model_add_line... INFO @ Tue, 16 Jun 2020 09:31:12: start X-correlation... INFO @ Tue, 16 Jun 2020 09:31:12: end of X-cor INFO @ Tue, 16 Jun 2020 09:31:12: #2 finished! INFO @ Tue, 16 Jun 2020 09:31:12: #2 predicted fragment length is 106 bps INFO @ Tue, 16 Jun 2020 09:31:12: #2 alternative fragment length(s) may be 3,84,106 bps INFO @ Tue, 16 Jun 2020 09:31:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085341/SRX4085341.20_model.r INFO @ Tue, 16 Jun 2020 09:31:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:31:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:31:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:31:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085341/SRX4085341.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:31:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085341/SRX4085341.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:31:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085341/SRX4085341.20_summits.bed INFO @ Tue, 16 Jun 2020 09:31:56: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (342 records, 4 fields): 2 millis CompletedMACS2peakCalling