Job ID = 5720196 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 16,295,947 reads read : 32,591,894 reads written : 32,591,894 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:32:43 16295947 reads; of these: 16295947 (100.00%) were paired; of these: 6011977 (36.89%) aligned concordantly 0 times 8680575 (53.27%) aligned concordantly exactly 1 time 1603395 (9.84%) aligned concordantly >1 times ---- 6011977 pairs aligned concordantly 0 times; of these: 3667516 (61.00%) aligned discordantly 1 time ---- 2344461 pairs aligned 0 times concordantly or discordantly; of these: 4688922 mates make up the pairs; of these: 3427896 (73.11%) aligned 0 times 533781 (11.38%) aligned exactly 1 time 727245 (15.51%) aligned >1 times 89.48% overall alignment rate Time searching: 00:32:43 Overall time: 00:32:43 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] 900650 / 13709523 = 0.0657 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 @ Wed, 15 Apr 2020 22:36:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6619565/SRX6619565.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6619565/SRX6619565.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6619565/SRX6619565.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6619565/SRX6619565.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, 15 Apr 2020 22:36:24: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:36:24: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:36:31: 1000000 INFO @ Wed, 15 Apr 2020 22:36:38: 2000000 INFO @ Wed, 15 Apr 2020 22:36:45: 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 @ Wed, 15 Apr 2020 22:36:52: 4000000 INFO @ Wed, 15 Apr 2020 22:36:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6619565/SRX6619565.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6619565/SRX6619565.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6619565/SRX6619565.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6619565/SRX6619565.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, 15 Apr 2020 22:36:54: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:36:54: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:37:00: 5000000 INFO @ Wed, 15 Apr 2020 22:37:02: 1000000 INFO @ Wed, 15 Apr 2020 22:37:08: 6000000 INFO @ Wed, 15 Apr 2020 22:37:10: 2000000 INFO @ Wed, 15 Apr 2020 22:37:17: 7000000 INFO @ Wed, 15 Apr 2020 22:37:18: 3000000 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 @ Wed, 15 Apr 2020 22:37:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6619565/SRX6619565.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6619565/SRX6619565.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6619565/SRX6619565.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6619565/SRX6619565.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, 15 Apr 2020 22:37:24: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:37:24: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:37:25: 8000000 INFO @ Wed, 15 Apr 2020 22:37:27: 4000000 INFO @ Wed, 15 Apr 2020 22:37:34: 9000000 INFO @ Wed, 15 Apr 2020 22:37:35: 1000000 INFO @ Wed, 15 Apr 2020 22:37:36: 5000000 INFO @ Wed, 15 Apr 2020 22:37:43: 10000000 INFO @ Wed, 15 Apr 2020 22:37:45: 6000000 INFO @ Wed, 15 Apr 2020 22:37:45: 2000000 INFO @ Wed, 15 Apr 2020 22:37:53: 11000000 INFO @ Wed, 15 Apr 2020 22:37:55: 7000000 INFO @ Wed, 15 Apr 2020 22:37:56: 3000000 INFO @ Wed, 15 Apr 2020 22:38:02: 12000000 INFO @ Wed, 15 Apr 2020 22:38:04: 8000000 INFO @ Wed, 15 Apr 2020 22:38:07: 4000000 INFO @ Wed, 15 Apr 2020 22:38:11: 13000000 INFO @ Wed, 15 Apr 2020 22:38:13: 9000000 INFO @ Wed, 15 Apr 2020 22:38:20: 14000000 INFO @ Wed, 15 Apr 2020 22:38:21: 5000000 INFO @ Wed, 15 Apr 2020 22:38:22: 10000000 INFO @ Wed, 15 Apr 2020 22:38:29: 15000000 INFO @ Wed, 15 Apr 2020 22:38:31: 11000000 INFO @ Wed, 15 Apr 2020 22:38:37: 6000000 INFO @ Wed, 15 Apr 2020 22:38:38: 16000000 INFO @ Wed, 15 Apr 2020 22:38:40: 12000000 INFO @ Wed, 15 Apr 2020 22:38:47: 17000000 INFO @ Wed, 15 Apr 2020 22:38:49: 13000000 INFO @ Wed, 15 Apr 2020 22:38:52: 7000000 INFO @ Wed, 15 Apr 2020 22:38:56: 18000000 INFO @ Wed, 15 Apr 2020 22:38:58: 14000000 INFO @ Wed, 15 Apr 2020 22:39:05: 19000000 INFO @ Wed, 15 Apr 2020 22:39:05: 8000000 INFO @ Wed, 15 Apr 2020 22:39:07: 15000000 INFO @ Wed, 15 Apr 2020 22:39:14: 20000000 INFO @ Wed, 15 Apr 2020 22:39:16: 9000000 INFO @ Wed, 15 Apr 2020 22:39:17: 16000000 INFO @ Wed, 15 Apr 2020 22:39:23: 21000000 INFO @ Wed, 15 Apr 2020 22:39:26: 17000000 INFO @ Wed, 15 Apr 2020 22:39:26: 10000000 INFO @ Wed, 15 Apr 2020 22:39:32: 22000000 INFO @ Wed, 15 Apr 2020 22:39:35: 18000000 INFO @ Wed, 15 Apr 2020 22:39:37: 11000000 INFO @ Wed, 15 Apr 2020 22:39:41: 23000000 INFO @ Wed, 15 Apr 2020 22:39:44: 19000000 INFO @ Wed, 15 Apr 2020 22:39:48: 12000000 INFO @ Wed, 15 Apr 2020 22:39:50: 24000000 INFO @ Wed, 15 Apr 2020 22:39:53: 20000000 INFO @ Wed, 15 Apr 2020 22:39:59: 13000000 INFO @ Wed, 15 Apr 2020 22:39:59: 25000000 INFO @ Wed, 15 Apr 2020 22:40:02: 21000000 INFO @ Wed, 15 Apr 2020 22:40:08: 26000000 INFO @ Wed, 15 Apr 2020 22:40:10: 14000000 INFO @ Wed, 15 Apr 2020 22:40:11: 22000000 INFO @ Wed, 15 Apr 2020 22:40:18: 27000000 INFO @ Wed, 15 Apr 2020 22:40:20: 15000000 INFO @ Wed, 15 Apr 2020 22:40:20: 23000000 INFO @ Wed, 15 Apr 2020 22:40:21: #1 tag size is determined as 150 bps INFO @ Wed, 15 Apr 2020 22:40:21: #1 tag size = 150 INFO @ Wed, 15 Apr 2020 22:40:21: #1 total tags in treatment: 9583151 INFO @ Wed, 15 Apr 2020 22:40:21: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:40:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:40:21: #1 tags after filtering in treatment: 8567255 INFO @ Wed, 15 Apr 2020 22:40:21: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 15 Apr 2020 22:40:21: #1 finished! INFO @ Wed, 15 Apr 2020 22:40:21: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:40:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:40:22: #2 number of paired peaks: 285 WARNING @ Wed, 15 Apr 2020 22:40:22: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Wed, 15 Apr 2020 22:40:22: start model_add_line... INFO @ Wed, 15 Apr 2020 22:40:22: start X-correlation... INFO @ Wed, 15 Apr 2020 22:40:22: end of X-cor INFO @ Wed, 15 Apr 2020 22:40:22: #2 finished! INFO @ Wed, 15 Apr 2020 22:40:22: #2 predicted fragment length is 208 bps INFO @ Wed, 15 Apr 2020 22:40:22: #2 alternative fragment length(s) may be 208 bps INFO @ Wed, 15 Apr 2020 22:40:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6619565/SRX6619565.05_model.r WARNING @ Wed, 15 Apr 2020 22:40:22: #2 Since the d (208) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 22:40:22: #2 You may need to consider one of the other alternative d(s): 208 WARNING @ Wed, 15 Apr 2020 22:40:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 22:40:22: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:40:22: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:40:29: 24000000 INFO @ Wed, 15 Apr 2020 22:40:30: 16000000 INFO @ Wed, 15 Apr 2020 22:40:38: 25000000 INFO @ Wed, 15 Apr 2020 22:40:40: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:40:42: 17000000 INFO @ Wed, 15 Apr 2020 22:40:47: 26000000 INFO @ Wed, 15 Apr 2020 22:40:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6619565/SRX6619565.05_peaks.xls INFO @ Wed, 15 Apr 2020 22:40:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6619565/SRX6619565.05_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:40:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6619565/SRX6619565.05_summits.bed INFO @ Wed, 15 Apr 2020 22:40:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (379 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 22:40:52: 18000000 INFO @ Wed, 15 Apr 2020 22:40:56: 27000000 INFO @ Wed, 15 Apr 2020 22:40:59: #1 tag size is determined as 150 bps INFO @ Wed, 15 Apr 2020 22:40:59: #1 tag size = 150 INFO @ Wed, 15 Apr 2020 22:40:59: #1 total tags in treatment: 9583151 INFO @ Wed, 15 Apr 2020 22:40:59: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:40:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:40:59: #1 tags after filtering in treatment: 8567255 INFO @ Wed, 15 Apr 2020 22:40:59: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 15 Apr 2020 22:40:59: #1 finished! INFO @ Wed, 15 Apr 2020 22:40:59: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:40:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:41:00: #2 number of paired peaks: 285 WARNING @ Wed, 15 Apr 2020 22:41:00: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Wed, 15 Apr 2020 22:41:00: start model_add_line... INFO @ Wed, 15 Apr 2020 22:41:00: start X-correlation... INFO @ Wed, 15 Apr 2020 22:41:00: end of X-cor INFO @ Wed, 15 Apr 2020 22:41:00: #2 finished! INFO @ Wed, 15 Apr 2020 22:41:00: #2 predicted fragment length is 208 bps INFO @ Wed, 15 Apr 2020 22:41:00: #2 alternative fragment length(s) may be 208 bps INFO @ Wed, 15 Apr 2020 22:41:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6619565/SRX6619565.10_model.r WARNING @ Wed, 15 Apr 2020 22:41:00: #2 Since the d (208) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 22:41:00: #2 You may need to consider one of the other alternative d(s): 208 WARNING @ Wed, 15 Apr 2020 22:41:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 22:41:00: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:41:00: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:41:02: 19000000 INFO @ Wed, 15 Apr 2020 22:41:12: 20000000 INFO @ Wed, 15 Apr 2020 22:41:17: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:41:21: 21000000 INFO @ Wed, 15 Apr 2020 22:41:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6619565/SRX6619565.10_peaks.xls INFO @ Wed, 15 Apr 2020 22:41:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6619565/SRX6619565.10_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:41:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6619565/SRX6619565.10_summits.bed INFO @ Wed, 15 Apr 2020 22:41:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (275 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 22:41:30: 22000000 INFO @ Wed, 15 Apr 2020 22:41:40: 23000000 INFO @ Wed, 15 Apr 2020 22:41:49: 24000000 INFO @ Wed, 15 Apr 2020 22:42:02: 25000000 INFO @ Wed, 15 Apr 2020 22:42:11: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 15 Apr 2020 22:42:21: 27000000 INFO @ Wed, 15 Apr 2020 22:42:24: #1 tag size is determined as 150 bps INFO @ Wed, 15 Apr 2020 22:42:24: #1 tag size = 150 INFO @ Wed, 15 Apr 2020 22:42:24: #1 total tags in treatment: 9583151 INFO @ Wed, 15 Apr 2020 22:42:24: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:42:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:42:24: #1 tags after filtering in treatment: 8567255 INFO @ Wed, 15 Apr 2020 22:42:24: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 15 Apr 2020 22:42:24: #1 finished! INFO @ Wed, 15 Apr 2020 22:42:24: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:42:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:42:25: #2 number of paired peaks: 285 WARNING @ Wed, 15 Apr 2020 22:42:25: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Wed, 15 Apr 2020 22:42:25: start model_add_line... INFO @ Wed, 15 Apr 2020 22:42:25: start X-correlation... INFO @ Wed, 15 Apr 2020 22:42:25: end of X-cor INFO @ Wed, 15 Apr 2020 22:42:25: #2 finished! INFO @ Wed, 15 Apr 2020 22:42:25: #2 predicted fragment length is 208 bps INFO @ Wed, 15 Apr 2020 22:42:25: #2 alternative fragment length(s) may be 208 bps INFO @ Wed, 15 Apr 2020 22:42:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6619565/SRX6619565.20_model.r WARNING @ Wed, 15 Apr 2020 22:42:25: #2 Since the d (208) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 22:42:25: #2 You may need to consider one of the other alternative d(s): 208 WARNING @ Wed, 15 Apr 2020 22:42:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 22:42:25: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:42:25: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:42:43: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:42:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6619565/SRX6619565.20_peaks.xls INFO @ Wed, 15 Apr 2020 22:42:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6619565/SRX6619565.20_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:42:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6619565/SRX6619565.20_summits.bed INFO @ Wed, 15 Apr 2020 22:42:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (177 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。