Job ID = 6367718 SRX = SRX4029334 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:34:20 prefetch.2.10.7: 1) Downloading 'SRR7100994'... 2020-06-15T23:34:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:45:58 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:45:59 prefetch.2.10.7: 1) 'SRR7100994' was downloaded successfully 2020-06-15T23:45:59 prefetch.2.10.7: 'SRR7100994' has 0 unresolved dependencies Read 27766032 spots for SRR7100994/SRR7100994.sra Written 27766032 spots for SRR7100994/SRR7100994.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: 00:35:43 27766032 reads; of these: 27766032 (100.00%) were paired; of these: 6613177 (23.82%) aligned concordantly 0 times 18727191 (67.45%) aligned concordantly exactly 1 time 2425664 (8.74%) aligned concordantly >1 times ---- 6613177 pairs aligned concordantly 0 times; of these: 2809222 (42.48%) aligned discordantly 1 time ---- 3803955 pairs aligned 0 times concordantly or discordantly; of these: 7607910 mates make up the pairs; of these: 5694127 (74.84%) aligned 0 times 1210679 (15.91%) aligned exactly 1 time 703104 (9.24%) aligned >1 times 89.75% overall alignment rate Time searching: 00:35:43 Overall time: 00:35:43 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] 7498192 / 23940074 = 0.3132 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 09:44:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4029334/SRX4029334.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4029334/SRX4029334.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4029334/SRX4029334.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4029334/SRX4029334.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 09:44:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:44:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:44:34: 1000000 INFO @ Tue, 16 Jun 2020 09:44:41: 2000000 INFO @ Tue, 16 Jun 2020 09:44:47: 3000000 INFO @ Tue, 16 Jun 2020 09:44:53: 4000000 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 09:44:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4029334/SRX4029334.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4029334/SRX4029334.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4029334/SRX4029334.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4029334/SRX4029334.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 09:44:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:44:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:44:59: 5000000 INFO @ Tue, 16 Jun 2020 09:45:04: 1000000 INFO @ Tue, 16 Jun 2020 09:45:06: 6000000 INFO @ Tue, 16 Jun 2020 09:45:11: 2000000 INFO @ Tue, 16 Jun 2020 09:45:13: 7000000 INFO @ Tue, 16 Jun 2020 09:45:18: 3000000 INFO @ Tue, 16 Jun 2020 09:45:20: 8000000 INFO @ Tue, 16 Jun 2020 09:45:25: 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 09:45:27: 9000000 INFO @ Tue, 16 Jun 2020 09:45:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4029334/SRX4029334.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4029334/SRX4029334.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4029334/SRX4029334.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4029334/SRX4029334.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 09:45:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:45:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:45:32: 5000000 INFO @ Tue, 16 Jun 2020 09:45:34: 10000000 INFO @ Tue, 16 Jun 2020 09:45:36: 1000000 INFO @ Tue, 16 Jun 2020 09:45:39: 6000000 INFO @ Tue, 16 Jun 2020 09:45:41: 11000000 INFO @ Tue, 16 Jun 2020 09:45:44: 2000000 INFO @ Tue, 16 Jun 2020 09:45:46: 7000000 INFO @ Tue, 16 Jun 2020 09:45:48: 12000000 INFO @ Tue, 16 Jun 2020 09:45:52: 3000000 INFO @ Tue, 16 Jun 2020 09:45:53: 8000000 INFO @ Tue, 16 Jun 2020 09:45:55: 13000000 INFO @ Tue, 16 Jun 2020 09:46:00: 4000000 INFO @ Tue, 16 Jun 2020 09:46:01: 9000000 INFO @ Tue, 16 Jun 2020 09:46:02: 14000000 INFO @ Tue, 16 Jun 2020 09:46:08: 10000000 INFO @ Tue, 16 Jun 2020 09:46:09: 5000000 INFO @ Tue, 16 Jun 2020 09:46:10: 15000000 INFO @ Tue, 16 Jun 2020 09:46:15: 11000000 INFO @ Tue, 16 Jun 2020 09:46:17: 6000000 INFO @ Tue, 16 Jun 2020 09:46:18: 16000000 INFO @ Tue, 16 Jun 2020 09:46:22: 12000000 INFO @ Tue, 16 Jun 2020 09:46:26: 7000000 INFO @ Tue, 16 Jun 2020 09:46:26: 17000000 INFO @ Tue, 16 Jun 2020 09:46:29: 13000000 INFO @ Tue, 16 Jun 2020 09:46:34: 8000000 INFO @ Tue, 16 Jun 2020 09:46:34: 18000000 INFO @ Tue, 16 Jun 2020 09:46:36: 14000000 INFO @ Tue, 16 Jun 2020 09:46:42: 9000000 INFO @ Tue, 16 Jun 2020 09:46:42: 19000000 INFO @ Tue, 16 Jun 2020 09:46:45: 15000000 INFO @ Tue, 16 Jun 2020 09:46:50: 10000000 INFO @ Tue, 16 Jun 2020 09:46:51: 20000000 INFO @ Tue, 16 Jun 2020 09:46:53: 16000000 INFO @ Tue, 16 Jun 2020 09:46:59: 11000000 INFO @ Tue, 16 Jun 2020 09:46:59: 21000000 INFO @ Tue, 16 Jun 2020 09:47:02: 17000000 INFO @ Tue, 16 Jun 2020 09:47:07: 22000000 INFO @ Tue, 16 Jun 2020 09:47:07: 12000000 INFO @ Tue, 16 Jun 2020 09:47:10: 18000000 INFO @ Tue, 16 Jun 2020 09:47:15: 23000000 INFO @ Tue, 16 Jun 2020 09:47:16: 13000000 INFO @ Tue, 16 Jun 2020 09:47:18: 19000000 INFO @ Tue, 16 Jun 2020 09:47:22: 24000000 INFO @ Tue, 16 Jun 2020 09:47:24: 14000000 INFO @ Tue, 16 Jun 2020 09:47:25: 20000000 INFO @ Tue, 16 Jun 2020 09:47:29: 25000000 INFO @ Tue, 16 Jun 2020 09:47:31: 15000000 INFO @ Tue, 16 Jun 2020 09:47:32: 21000000 INFO @ Tue, 16 Jun 2020 09:47:37: 26000000 INFO @ Tue, 16 Jun 2020 09:47:39: 16000000 INFO @ Tue, 16 Jun 2020 09:47:39: 22000000 INFO @ Tue, 16 Jun 2020 09:47:44: 27000000 INFO @ Tue, 16 Jun 2020 09:47:46: 17000000 INFO @ Tue, 16 Jun 2020 09:47:46: 23000000 INFO @ Tue, 16 Jun 2020 09:47:51: 28000000 INFO @ Tue, 16 Jun 2020 09:47:53: 18000000 INFO @ Tue, 16 Jun 2020 09:47:54: 24000000 INFO @ Tue, 16 Jun 2020 09:47:58: 29000000 INFO @ Tue, 16 Jun 2020 09:48:01: 25000000 INFO @ Tue, 16 Jun 2020 09:48:02: 19000000 INFO @ Tue, 16 Jun 2020 09:48:05: 30000000 INFO @ Tue, 16 Jun 2020 09:48:08: 26000000 INFO @ Tue, 16 Jun 2020 09:48:10: 20000000 INFO @ Tue, 16 Jun 2020 09:48:13: 31000000 INFO @ Tue, 16 Jun 2020 09:48:15: 27000000 INFO @ Tue, 16 Jun 2020 09:48:18: 21000000 INFO @ Tue, 16 Jun 2020 09:48:20: 32000000 INFO @ Tue, 16 Jun 2020 09:48:22: 28000000 INFO @ Tue, 16 Jun 2020 09:48:26: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:48:27: 33000000 INFO @ Tue, 16 Jun 2020 09:48:30: 29000000 INFO @ Tue, 16 Jun 2020 09:48:35: 34000000 INFO @ Tue, 16 Jun 2020 09:48:35: 23000000 INFO @ Tue, 16 Jun 2020 09:48:37: 30000000 INFO @ Tue, 16 Jun 2020 09:48:41: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:48:41: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:48:41: #1 total tags in treatment: 14127532 INFO @ Tue, 16 Jun 2020 09:48:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:48:41: #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 09:48:41: #1 tags after filtering in treatment: 12103645 INFO @ Tue, 16 Jun 2020 09:48:41: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 16 Jun 2020 09:48:41: #1 finished! INFO @ Tue, 16 Jun 2020 09:48:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:48:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:48:42: #2 number of paired peaks: 523 WARNING @ Tue, 16 Jun 2020 09:48:42: Fewer paired peaks (523) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 523 pairs to build model! INFO @ Tue, 16 Jun 2020 09:48:42: start model_add_line... INFO @ Tue, 16 Jun 2020 09:48:42: start X-correlation... INFO @ Tue, 16 Jun 2020 09:48:42: end of X-cor INFO @ Tue, 16 Jun 2020 09:48:42: #2 finished! INFO @ Tue, 16 Jun 2020 09:48:42: #2 predicted fragment length is 181 bps INFO @ Tue, 16 Jun 2020 09:48:42: #2 alternative fragment length(s) may be 181 bps INFO @ Tue, 16 Jun 2020 09:48:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4029334/SRX4029334.05_model.r INFO @ Tue, 16 Jun 2020 09:48:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:48:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:48:44: 24000000 INFO @ Tue, 16 Jun 2020 09:48:44: 31000000 INFO @ Tue, 16 Jun 2020 09:48:51: 32000000 INFO @ Tue, 16 Jun 2020 09:48:53: 25000000 INFO @ Tue, 16 Jun 2020 09:48:59: 33000000 INFO @ Tue, 16 Jun 2020 09:49:01: 26000000 INFO @ Tue, 16 Jun 2020 09:49:06: 34000000 INFO @ Tue, 16 Jun 2020 09:49:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:49:10: 27000000 INFO @ Tue, 16 Jun 2020 09:49:12: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:49:12: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:49:12: #1 total tags in treatment: 14127532 INFO @ Tue, 16 Jun 2020 09:49:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:49:12: #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 09:49:12: #1 tags after filtering in treatment: 12103645 INFO @ Tue, 16 Jun 2020 09:49:12: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 16 Jun 2020 09:49:12: #1 finished! INFO @ Tue, 16 Jun 2020 09:49:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:49:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:49:13: #2 number of paired peaks: 523 WARNING @ Tue, 16 Jun 2020 09:49:13: Fewer paired peaks (523) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 523 pairs to build model! INFO @ Tue, 16 Jun 2020 09:49:13: start model_add_line... INFO @ Tue, 16 Jun 2020 09:49:13: start X-correlation... INFO @ Tue, 16 Jun 2020 09:49:13: end of X-cor INFO @ Tue, 16 Jun 2020 09:49:13: #2 finished! INFO @ Tue, 16 Jun 2020 09:49:13: #2 predicted fragment length is 181 bps INFO @ Tue, 16 Jun 2020 09:49:13: #2 alternative fragment length(s) may be 181 bps INFO @ Tue, 16 Jun 2020 09:49:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4029334/SRX4029334.10_model.r INFO @ Tue, 16 Jun 2020 09:49:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:49:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:49:18: 28000000 INFO @ Tue, 16 Jun 2020 09:49:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4029334/SRX4029334.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:49:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4029334/SRX4029334.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:49:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4029334/SRX4029334.05_summits.bed INFO @ Tue, 16 Jun 2020 09:49:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3357 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:49:26: 29000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:49:34: 30000000 INFO @ Tue, 16 Jun 2020 09:49:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:49:42: 31000000 INFO @ Tue, 16 Jun 2020 09:49:50: 32000000 INFO @ Tue, 16 Jun 2020 09:49:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4029334/SRX4029334.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:49:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4029334/SRX4029334.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:49:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4029334/SRX4029334.10_summits.bed INFO @ Tue, 16 Jun 2020 09:49:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1941 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:49:57: 33000000 INFO @ Tue, 16 Jun 2020 09:50:05: 34000000 INFO @ Tue, 16 Jun 2020 09:50:11: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:50:11: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:50:11: #1 total tags in treatment: 14127532 INFO @ Tue, 16 Jun 2020 09:50:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:50:11: #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 09:50:11: #1 tags after filtering in treatment: 12103645 INFO @ Tue, 16 Jun 2020 09:50:11: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 16 Jun 2020 09:50:11: #1 finished! INFO @ Tue, 16 Jun 2020 09:50:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:50:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:50:12: #2 number of paired peaks: 523 WARNING @ Tue, 16 Jun 2020 09:50:12: Fewer paired peaks (523) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 523 pairs to build model! INFO @ Tue, 16 Jun 2020 09:50:12: start model_add_line... INFO @ Tue, 16 Jun 2020 09:50:12: start X-correlation... INFO @ Tue, 16 Jun 2020 09:50:12: end of X-cor INFO @ Tue, 16 Jun 2020 09:50:12: #2 finished! INFO @ Tue, 16 Jun 2020 09:50:12: #2 predicted fragment length is 181 bps INFO @ Tue, 16 Jun 2020 09:50:12: #2 alternative fragment length(s) may be 181 bps INFO @ Tue, 16 Jun 2020 09:50:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4029334/SRX4029334.20_model.r INFO @ Tue, 16 Jun 2020 09:50:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:50:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:50:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:50:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4029334/SRX4029334.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:50:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4029334/SRX4029334.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:50:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4029334/SRX4029334.20_summits.bed INFO @ Tue, 16 Jun 2020 09:50:55: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (863 records, 4 fields): 2 millis CompletedMACS2peakCalling