Job ID = 6368869 SRX = SRX6619567 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-16T00:37:31 prefetch.2.10.7: 1) Downloading 'SRR9866042'... 2020-06-16T00:37:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:50:30 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:50:30 prefetch.2.10.7: 1) 'SRR9866042' was downloaded successfully 2020-06-16T00:50:30 prefetch.2.10.7: 'SRR9866042' has 0 unresolved dependencies Read 25253342 spots for SRR9866042/SRR9866042.sra Written 25253342 spots for SRR9866042/SRR9866042.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: 00:56:23 25253342 reads; of these: 25253342 (100.00%) were paired; of these: 11845889 (46.91%) aligned concordantly 0 times 10485376 (41.52%) aligned concordantly exactly 1 time 2922077 (11.57%) aligned concordantly >1 times ---- 11845889 pairs aligned concordantly 0 times; of these: 6191027 (52.26%) aligned discordantly 1 time ---- 5654862 pairs aligned 0 times concordantly or discordantly; of these: 11309724 mates make up the pairs; of these: 8580117 (75.86%) aligned 0 times 977421 (8.64%) aligned exactly 1 time 1752186 (15.49%) aligned >1 times 83.01% overall alignment rate Time searching: 00:56:23 Overall time: 00:56:23 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 32 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] 2281292 / 19131272 = 0.1192 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 11:13:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6619567/SRX6619567.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6619567/SRX6619567.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6619567/SRX6619567.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6619567/SRX6619567.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 11:13:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 11:13:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 11:14:06: 1000000 INFO @ Tue, 16 Jun 2020 11:14:18: 2000000 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 11:14:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6619567/SRX6619567.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6619567/SRX6619567.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6619567/SRX6619567.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6619567/SRX6619567.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 11:14:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 11:14:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 11:14:31: 3000000 INFO @ Tue, 16 Jun 2020 11:14:37: 1000000 INFO @ Tue, 16 Jun 2020 11:14:45: 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 11:14:52: 2000000 INFO @ Tue, 16 Jun 2020 11:14:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6619567/SRX6619567.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6619567/SRX6619567.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6619567/SRX6619567.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6619567/SRX6619567.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 11:14:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 11:14:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 11:15:00: 5000000 INFO @ Tue, 16 Jun 2020 11:15:06: 1000000 INFO @ Tue, 16 Jun 2020 11:15:08: 3000000 INFO @ Tue, 16 Jun 2020 11:15:16: 6000000 INFO @ Tue, 16 Jun 2020 11:15:20: 2000000 INFO @ Tue, 16 Jun 2020 11:15:24: 4000000 INFO @ Tue, 16 Jun 2020 11:15:32: 7000000 INFO @ Tue, 16 Jun 2020 11:15:35: 3000000 INFO @ Tue, 16 Jun 2020 11:15:40: 5000000 INFO @ Tue, 16 Jun 2020 11:15:47: 8000000 INFO @ Tue, 16 Jun 2020 11:15:48: 4000000 INFO @ Tue, 16 Jun 2020 11:15:55: 6000000 INFO @ Tue, 16 Jun 2020 11:16:01: 5000000 INFO @ Tue, 16 Jun 2020 11:16:03: 9000000 INFO @ Tue, 16 Jun 2020 11:16:11: 7000000 INFO @ Tue, 16 Jun 2020 11:16:15: 6000000 INFO @ Tue, 16 Jun 2020 11:16:18: 10000000 INFO @ Tue, 16 Jun 2020 11:16:26: 8000000 INFO @ Tue, 16 Jun 2020 11:16:29: 7000000 INFO @ Tue, 16 Jun 2020 11:16:34: 11000000 INFO @ Tue, 16 Jun 2020 11:16:42: 9000000 INFO @ Tue, 16 Jun 2020 11:16:42: 8000000 INFO @ Tue, 16 Jun 2020 11:16:50: 12000000 INFO @ Tue, 16 Jun 2020 11:16:56: 9000000 INFO @ Tue, 16 Jun 2020 11:16:57: 10000000 INFO @ Tue, 16 Jun 2020 11:17:05: 13000000 INFO @ Tue, 16 Jun 2020 11:17:10: 10000000 INFO @ Tue, 16 Jun 2020 11:17:13: 11000000 INFO @ Tue, 16 Jun 2020 11:17:21: 14000000 INFO @ Tue, 16 Jun 2020 11:17:23: 11000000 INFO @ Tue, 16 Jun 2020 11:17:29: 12000000 INFO @ Tue, 16 Jun 2020 11:17:36: 15000000 INFO @ Tue, 16 Jun 2020 11:17:37: 12000000 INFO @ Tue, 16 Jun 2020 11:17:44: 13000000 INFO @ Tue, 16 Jun 2020 11:17:51: 13000000 INFO @ Tue, 16 Jun 2020 11:17:52: 16000000 INFO @ Tue, 16 Jun 2020 11:18:00: 14000000 INFO @ Tue, 16 Jun 2020 11:18:04: 14000000 INFO @ Tue, 16 Jun 2020 11:18:07: 17000000 INFO @ Tue, 16 Jun 2020 11:18:14: 15000000 INFO @ Tue, 16 Jun 2020 11:18:18: 15000000 INFO @ Tue, 16 Jun 2020 11:18:22: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 11:18:29: 16000000 INFO @ Tue, 16 Jun 2020 11:18:32: 16000000 INFO @ Tue, 16 Jun 2020 11:18:36: 19000000 INFO @ Tue, 16 Jun 2020 11:18:43: 17000000 INFO @ Tue, 16 Jun 2020 11:18:45: 17000000 INFO @ Tue, 16 Jun 2020 11:18:51: 20000000 INFO @ Tue, 16 Jun 2020 11:18:58: 18000000 INFO @ Tue, 16 Jun 2020 11:18:59: 18000000 INFO @ Tue, 16 Jun 2020 11:19:05: 21000000 INFO @ Tue, 16 Jun 2020 11:19:13: 19000000 INFO @ Tue, 16 Jun 2020 11:19:13: 19000000 INFO @ Tue, 16 Jun 2020 11:19:19: 22000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 11:19:28: 20000000 INFO @ Tue, 16 Jun 2020 11:19:28: 20000000 INFO @ Tue, 16 Jun 2020 11:19:34: 23000000 INFO @ Tue, 16 Jun 2020 11:19:43: 21000000 INFO @ Tue, 16 Jun 2020 11:19:43: 21000000 INFO @ Tue, 16 Jun 2020 11:19:49: 24000000 INFO @ Tue, 16 Jun 2020 11:19:58: 22000000 INFO @ Tue, 16 Jun 2020 11:19:58: 22000000 INFO @ Tue, 16 Jun 2020 11:20:03: 25000000 INFO @ Tue, 16 Jun 2020 11:20:12: 23000000 INFO @ Tue, 16 Jun 2020 11:20:12: 23000000 INFO @ Tue, 16 Jun 2020 11:20:17: 26000000 INFO @ Tue, 16 Jun 2020 11:20:25: 24000000 INFO @ Tue, 16 Jun 2020 11:20:26: 24000000 INFO @ Tue, 16 Jun 2020 11:20:32: 27000000 INFO @ Tue, 16 Jun 2020 11:20:38: 25000000 INFO @ Tue, 16 Jun 2020 11:20:40: 25000000 INFO @ Tue, 16 Jun 2020 11:20:46: 28000000 INFO @ Tue, 16 Jun 2020 11:20:52: 26000000 INFO @ Tue, 16 Jun 2020 11:20:55: 26000000 INFO @ Tue, 16 Jun 2020 11:21:01: 29000000 INFO @ Tue, 16 Jun 2020 11:21:06: 27000000 INFO @ Tue, 16 Jun 2020 11:21:09: 27000000 INFO @ Tue, 16 Jun 2020 11:21:15: 30000000 INFO @ Tue, 16 Jun 2020 11:21:20: 28000000 INFO @ Tue, 16 Jun 2020 11:21:24: 28000000 INFO @ Tue, 16 Jun 2020 11:21:30: 31000000 INFO @ Tue, 16 Jun 2020 11:21:33: 29000000 INFO @ Tue, 16 Jun 2020 11:21:37: 29000000 INFO @ Tue, 16 Jun 2020 11:21:41: 32000000 INFO @ Tue, 16 Jun 2020 11:21:44: 30000000 INFO @ Tue, 16 Jun 2020 11:21:48: 30000000 INFO @ Tue, 16 Jun 2020 11:21:53: 33000000 INFO @ Tue, 16 Jun 2020 11:21:55: 31000000 INFO @ Tue, 16 Jun 2020 11:22:00: 31000000 INFO @ Tue, 16 Jun 2020 11:22:04: 34000000 INFO @ Tue, 16 Jun 2020 11:22:05: 32000000 INFO @ Tue, 16 Jun 2020 11:22:11: 32000000 INFO @ Tue, 16 Jun 2020 11:22:16: 35000000 INFO @ Tue, 16 Jun 2020 11:22:16: 33000000 INFO @ Tue, 16 Jun 2020 11:22:22: 33000000 INFO @ Tue, 16 Jun 2020 11:22:27: 36000000 INFO @ Tue, 16 Jun 2020 11:22:27: 34000000 INFO @ Tue, 16 Jun 2020 11:22:33: 34000000 INFO @ Tue, 16 Jun 2020 11:22:38: 37000000 INFO @ Tue, 16 Jun 2020 11:22:38: 35000000 INFO @ Tue, 16 Jun 2020 11:22:42: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 11:22:42: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 11:22:42: #1 total tags in treatment: 11657501 INFO @ Tue, 16 Jun 2020 11:22:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 11:22:42: #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 11:22:42: #1 tags after filtering in treatment: 9680845 INFO @ Tue, 16 Jun 2020 11:22:42: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 16 Jun 2020 11:22:42: #1 finished! INFO @ Tue, 16 Jun 2020 11:22:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 11:22:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 11:22:43: #2 number of paired peaks: 375 WARNING @ Tue, 16 Jun 2020 11:22:43: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Tue, 16 Jun 2020 11:22:43: start model_add_line... INFO @ Tue, 16 Jun 2020 11:22:43: start X-correlation... INFO @ Tue, 16 Jun 2020 11:22:43: end of X-cor INFO @ Tue, 16 Jun 2020 11:22:43: #2 finished! INFO @ Tue, 16 Jun 2020 11:22:43: #2 predicted fragment length is 199 bps INFO @ Tue, 16 Jun 2020 11:22:43: #2 alternative fragment length(s) may be 199,216 bps INFO @ Tue, 16 Jun 2020 11:22:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6619567/SRX6619567.05_model.r WARNING @ Tue, 16 Jun 2020 11:22:43: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 11:22:43: #2 You may need to consider one of the other alternative d(s): 199,216 WARNING @ Tue, 16 Jun 2020 11:22:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 11:22:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 11:22:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 11:22:44: 35000000 INFO @ Tue, 16 Jun 2020 11:22:49: 36000000 INFO @ Tue, 16 Jun 2020 11:22:55: 36000000 INFO @ Tue, 16 Jun 2020 11:23:00: 37000000 INFO @ Tue, 16 Jun 2020 11:23:04: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 11:23:04: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 11:23:04: #1 total tags in treatment: 11657501 INFO @ Tue, 16 Jun 2020 11:23:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 11:23:04: #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 11:23:04: #1 tags after filtering in treatment: 9680845 INFO @ Tue, 16 Jun 2020 11:23:04: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 16 Jun 2020 11:23:04: #1 finished! INFO @ Tue, 16 Jun 2020 11:23:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 11:23:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 11:23:05: #2 number of paired peaks: 375 WARNING @ Tue, 16 Jun 2020 11:23:05: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Tue, 16 Jun 2020 11:23:05: start model_add_line... INFO @ Tue, 16 Jun 2020 11:23:05: start X-correlation... INFO @ Tue, 16 Jun 2020 11:23:05: end of X-cor INFO @ Tue, 16 Jun 2020 11:23:05: #2 finished! INFO @ Tue, 16 Jun 2020 11:23:05: #2 predicted fragment length is 199 bps INFO @ Tue, 16 Jun 2020 11:23:05: #2 alternative fragment length(s) may be 199,216 bps INFO @ Tue, 16 Jun 2020 11:23:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6619567/SRX6619567.20_model.r WARNING @ Tue, 16 Jun 2020 11:23:05: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 11:23:05: #2 You may need to consider one of the other alternative d(s): 199,216 WARNING @ Tue, 16 Jun 2020 11:23:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 11:23:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 11:23:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 11:23:05: 37000000 INFO @ Tue, 16 Jun 2020 11:23:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 11:23:09: #1 tag size is determined as 150 bps INFO @ Tue, 16 Jun 2020 11:23:09: #1 tag size = 150 INFO @ Tue, 16 Jun 2020 11:23:09: #1 total tags in treatment: 11657501 INFO @ Tue, 16 Jun 2020 11:23:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 11:23:09: #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 11:23:09: #1 tags after filtering in treatment: 9680845 INFO @ Tue, 16 Jun 2020 11:23:09: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 16 Jun 2020 11:23:09: #1 finished! INFO @ Tue, 16 Jun 2020 11:23:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 11:23:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 11:23:10: #2 number of paired peaks: 375 WARNING @ Tue, 16 Jun 2020 11:23:10: Fewer paired peaks (375) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 375 pairs to build model! INFO @ Tue, 16 Jun 2020 11:23:10: start model_add_line... INFO @ Tue, 16 Jun 2020 11:23:10: start X-correlation... INFO @ Tue, 16 Jun 2020 11:23:10: end of X-cor INFO @ Tue, 16 Jun 2020 11:23:10: #2 finished! INFO @ Tue, 16 Jun 2020 11:23:10: #2 predicted fragment length is 199 bps INFO @ Tue, 16 Jun 2020 11:23:10: #2 alternative fragment length(s) may be 199,216 bps INFO @ Tue, 16 Jun 2020 11:23:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6619567/SRX6619567.10_model.r WARNING @ Tue, 16 Jun 2020 11:23:10: #2 Since the d (199) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 11:23:10: #2 You may need to consider one of the other alternative d(s): 199,216 WARNING @ Tue, 16 Jun 2020 11:23:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 11:23:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 11:23:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 11:23:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6619567/SRX6619567.05_peaks.xls INFO @ Tue, 16 Jun 2020 11:23:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6619567/SRX6619567.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 11:23:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6619567/SRX6619567.05_summits.bed INFO @ Tue, 16 Jun 2020 11:23:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (423 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 11:23:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 11:23:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 11:23:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6619567/SRX6619567.20_peaks.xls INFO @ Tue, 16 Jun 2020 11:23:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6619567/SRX6619567.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 11:23:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6619567/SRX6619567.20_summits.bed INFO @ Tue, 16 Jun 2020 11:23:38: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (188 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 11:23:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6619567/SRX6619567.10_peaks.xls INFO @ Tue, 16 Jun 2020 11:23:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6619567/SRX6619567.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 11:23:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6619567/SRX6619567.10_summits.bed INFO @ Tue, 16 Jun 2020 11:23:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (300 records, 4 fields): 1 millis CompletedMACS2peakCalling