Job ID = 8069438 SRX = SRX8392422 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T03:32:55 prefetch.2.10.7: 1) Downloading 'SRR11842075'... 2020-08-08T03:32:55 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:36:21 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:36:21 prefetch.2.10.7: 1) 'SRR11842075' was downloaded successfully 2020-08-08T03:36:21 prefetch.2.10.7: 'SRR11842075' has 0 unresolved dependencies Read 8452957 spots for SRR11842075/SRR11842075.sra Written 8452957 spots for SRR11842075/SRR11842075.sra fastq に変換しました。 bowtie でマッピング中... Your job 8070421 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:13:19 8452957 reads; of these: 8452957 (100.00%) were paired; of these: 2862877 (33.87%) aligned concordantly 0 times 4755064 (56.25%) aligned concordantly exactly 1 time 835016 (9.88%) aligned concordantly >1 times ---- 2862877 pairs aligned concordantly 0 times; of these: 948290 (33.12%) aligned discordantly 1 time ---- 1914587 pairs aligned 0 times concordantly or discordantly; of these: 3829174 mates make up the pairs; of these: 3503740 (91.50%) aligned 0 times 146167 (3.82%) aligned exactly 1 time 179267 (4.68%) aligned >1 times 79.28% overall alignment rate Time searching: 00:13:19 Overall time: 00:13:19 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] 1271696 / 6482867 = 0.1962 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 @ Sat, 08 Aug 2020 12:56:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392422/SRX8392422.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392422/SRX8392422.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392422/SRX8392422.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392422/SRX8392422.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 @ Sat, 08 Aug 2020 12:56:14: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:56:14: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:56:21: 1000000 INFO @ Sat, 08 Aug 2020 12:56:28: 2000000 INFO @ Sat, 08 Aug 2020 12:56:35: 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 @ Sat, 08 Aug 2020 12:56:42: 4000000 INFO @ Sat, 08 Aug 2020 12:56:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392422/SRX8392422.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392422/SRX8392422.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392422/SRX8392422.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392422/SRX8392422.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 @ Sat, 08 Aug 2020 12:56:44: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:56:44: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:56:51: 5000000 INFO @ Sat, 08 Aug 2020 12:56:54: 1000000 INFO @ Sat, 08 Aug 2020 12:57:00: 6000000 INFO @ Sat, 08 Aug 2020 12:57:05: 2000000 INFO @ Sat, 08 Aug 2020 12:57:09: 7000000 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 @ Sat, 08 Aug 2020 12:57:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392422/SRX8392422.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392422/SRX8392422.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392422/SRX8392422.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392422/SRX8392422.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 @ Sat, 08 Aug 2020 12:57:14: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:57:14: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:57:15: 3000000 INFO @ Sat, 08 Aug 2020 12:57:17: 8000000 INFO @ Sat, 08 Aug 2020 12:57:23: 1000000 INFO @ Sat, 08 Aug 2020 12:57:26: 4000000 INFO @ Sat, 08 Aug 2020 12:57:26: 9000000 INFO @ Sat, 08 Aug 2020 12:57:32: 2000000 INFO @ Sat, 08 Aug 2020 12:57:35: 10000000 INFO @ Sat, 08 Aug 2020 12:57:36: 5000000 INFO @ Sat, 08 Aug 2020 12:57:41: 3000000 INFO @ Sat, 08 Aug 2020 12:57:42: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:57:42: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:57:42: #1 total tags in treatment: 4465792 INFO @ Sat, 08 Aug 2020 12:57:42: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:57:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:57:43: #1 tags after filtering in treatment: 4129741 INFO @ Sat, 08 Aug 2020 12:57:43: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 12:57:43: #1 finished! INFO @ Sat, 08 Aug 2020 12:57:43: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:57:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:57:43: #2 number of paired peaks: 485 WARNING @ Sat, 08 Aug 2020 12:57:43: Fewer paired peaks (485) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 485 pairs to build model! INFO @ Sat, 08 Aug 2020 12:57:43: start model_add_line... INFO @ Sat, 08 Aug 2020 12:57:43: start X-correlation... INFO @ Sat, 08 Aug 2020 12:57:43: end of X-cor INFO @ Sat, 08 Aug 2020 12:57:43: #2 finished! INFO @ Sat, 08 Aug 2020 12:57:43: #2 predicted fragment length is 208 bps INFO @ Sat, 08 Aug 2020 12:57:43: #2 alternative fragment length(s) may be 208 bps INFO @ Sat, 08 Aug 2020 12:57:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392422/SRX8392422.05_model.r WARNING @ Sat, 08 Aug 2020 12:57:43: #2 Since the d (208) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:57:43: #2 You may need to consider one of the other alternative d(s): 208 WARNING @ Sat, 08 Aug 2020 12:57:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 12:57:43: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:57:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:57:47: 6000000 INFO @ Sat, 08 Aug 2020 12:57:50: 4000000 INFO @ Sat, 08 Aug 2020 12:57:52: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:57:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392422/SRX8392422.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:57:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392422/SRX8392422.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:57:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392422/SRX8392422.05_summits.bed INFO @ Sat, 08 Aug 2020 12:57:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (416 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:57:57: 7000000 INFO @ Sat, 08 Aug 2020 12:57:58: 5000000 INFO @ Sat, 08 Aug 2020 12:58:07: 6000000 INFO @ Sat, 08 Aug 2020 12:58:08: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 12:58:16: 7000000 INFO @ Sat, 08 Aug 2020 12:58:18: 9000000 INFO @ Sat, 08 Aug 2020 12:58:25: 8000000 INFO @ Sat, 08 Aug 2020 12:58:29: 10000000 INFO @ Sat, 08 Aug 2020 12:58:34: 9000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 12:58:38: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:58:38: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:58:38: #1 total tags in treatment: 4465792 INFO @ Sat, 08 Aug 2020 12:58:38: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:58:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:58:38: #1 tags after filtering in treatment: 4129741 INFO @ Sat, 08 Aug 2020 12:58:38: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 12:58:38: #1 finished! INFO @ Sat, 08 Aug 2020 12:58:38: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:58:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:58:38: #2 number of paired peaks: 485 WARNING @ Sat, 08 Aug 2020 12:58:38: Fewer paired peaks (485) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 485 pairs to build model! INFO @ Sat, 08 Aug 2020 12:58:38: start model_add_line... INFO @ Sat, 08 Aug 2020 12:58:38: start X-correlation... INFO @ Sat, 08 Aug 2020 12:58:38: end of X-cor INFO @ Sat, 08 Aug 2020 12:58:38: #2 finished! INFO @ Sat, 08 Aug 2020 12:58:38: #2 predicted fragment length is 208 bps INFO @ Sat, 08 Aug 2020 12:58:38: #2 alternative fragment length(s) may be 208 bps INFO @ Sat, 08 Aug 2020 12:58:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392422/SRX8392422.10_model.r WARNING @ Sat, 08 Aug 2020 12:58:38: #2 Since the d (208) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:58:38: #2 You may need to consider one of the other alternative d(s): 208 WARNING @ Sat, 08 Aug 2020 12:58:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 12:58:38: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:58:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:58:42: 10000000 INFO @ Sat, 08 Aug 2020 12:58:48: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:58:49: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:58:49: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:58:49: #1 total tags in treatment: 4465792 INFO @ Sat, 08 Aug 2020 12:58:49: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:58:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:58:49: #1 tags after filtering in treatment: 4129741 INFO @ Sat, 08 Aug 2020 12:58:49: #1 Redundant rate of treatment: 0.08 INFO @ Sat, 08 Aug 2020 12:58:49: #1 finished! INFO @ Sat, 08 Aug 2020 12:58:49: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:58:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:58:50: #2 number of paired peaks: 485 WARNING @ Sat, 08 Aug 2020 12:58:50: Fewer paired peaks (485) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 485 pairs to build model! INFO @ Sat, 08 Aug 2020 12:58:50: start model_add_line... INFO @ Sat, 08 Aug 2020 12:58:50: start X-correlation... INFO @ Sat, 08 Aug 2020 12:58:50: end of X-cor INFO @ Sat, 08 Aug 2020 12:58:50: #2 finished! INFO @ Sat, 08 Aug 2020 12:58:50: #2 predicted fragment length is 208 bps INFO @ Sat, 08 Aug 2020 12:58:50: #2 alternative fragment length(s) may be 208 bps INFO @ Sat, 08 Aug 2020 12:58:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392422/SRX8392422.20_model.r WARNING @ Sat, 08 Aug 2020 12:58:50: #2 Since the d (208) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:58:50: #2 You may need to consider one of the other alternative d(s): 208 WARNING @ Sat, 08 Aug 2020 12:58:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 12:58:50: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:58:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:58:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392422/SRX8392422.10_peaks.xls INFO @ Sat, 08 Aug 2020 12:58:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392422/SRX8392422.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:58:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392422/SRX8392422.10_summits.bed INFO @ Sat, 08 Aug 2020 12:58:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (257 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:58:59: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:59:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392422/SRX8392422.20_peaks.xls INFO @ Sat, 08 Aug 2020 12:59:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392422/SRX8392422.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:59:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392422/SRX8392422.20_summits.bed INFO @ Sat, 08 Aug 2020 12:59:04: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (180 records, 4 fields): 2 millis CompletedMACS2peakCalling