Job ID = 6369041 SRX = SRX982105 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:39:17 prefetch.2.10.7: 1) Downloading 'SRR1956593'... 2020-06-16T00:39:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:40:48 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:40:49 prefetch.2.10.7: 'SRR1956593' is valid 2020-06-16T00:40:49 prefetch.2.10.7: 1) 'SRR1956593' was downloaded successfully Read 8335869 spots for SRR1956593/SRR1956593.sra Written 8335869 spots for SRR1956593/SRR1956593.sra 2020-06-16T00:41:24 prefetch.2.10.7: 1) Downloading 'SRR1956594'... 2020-06-16T00:41:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:42:25 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:42:26 prefetch.2.10.7: 'SRR1956594' is valid 2020-06-16T00:42:26 prefetch.2.10.7: 1) 'SRR1956594' was downloaded successfully Read 8998757 spots for SRR1956594/SRR1956594.sra Written 8998757 spots for SRR1956594/SRR1956594.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: 00:03:50 17334626 reads; of these: 17334626 (100.00%) were unpaired; of these: 2050210 (11.83%) aligned 0 times 12804902 (73.87%) aligned exactly 1 time 2479514 (14.30%) aligned >1 times 88.17% overall alignment rate Time searching: 00:03:50 Overall time: 00:03:50 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 8 files... [bam_rmdupse_core] 1495707 / 15284416 = 0.0979 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 09:51:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982105/SRX982105.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982105/SRX982105.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982105/SRX982105.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982105/SRX982105.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 09:51:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:51:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:51:32: 1000000 INFO @ Tue, 16 Jun 2020 09:51:37: 2000000 INFO @ Tue, 16 Jun 2020 09:51:42: 3000000 INFO @ Tue, 16 Jun 2020 09:51:47: 4000000 INFO @ Tue, 16 Jun 2020 09:51:52: 5000000 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 09:51:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982105/SRX982105.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982105/SRX982105.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982105/SRX982105.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982105/SRX982105.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 09:51:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:51:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:51:57: 6000000 INFO @ Tue, 16 Jun 2020 09:52:02: 1000000 INFO @ Tue, 16 Jun 2020 09:52:03: 7000000 INFO @ Tue, 16 Jun 2020 09:52:08: 2000000 INFO @ Tue, 16 Jun 2020 09:52:08: 8000000 INFO @ Tue, 16 Jun 2020 09:52:13: 3000000 INFO @ Tue, 16 Jun 2020 09:52:14: 9000000 INFO @ Tue, 16 Jun 2020 09:52:19: 4000000 INFO @ Tue, 16 Jun 2020 09:52:19: 10000000 INFO @ Tue, 16 Jun 2020 09:52:24: 5000000 INFO @ Tue, 16 Jun 2020 09:52:25: 11000000 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 09:52:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982105/SRX982105.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982105/SRX982105.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982105/SRX982105.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982105/SRX982105.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 09:52:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:52:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:52:30: 6000000 INFO @ Tue, 16 Jun 2020 09:52:30: 12000000 INFO @ Tue, 16 Jun 2020 09:52:34: 1000000 INFO @ Tue, 16 Jun 2020 09:52:36: 7000000 INFO @ Tue, 16 Jun 2020 09:52:36: 13000000 INFO @ Tue, 16 Jun 2020 09:52:40: 2000000 INFO @ Tue, 16 Jun 2020 09:52:41: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:52:41: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:52:41: #1 total tags in treatment: 13788709 INFO @ Tue, 16 Jun 2020 09:52:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:52:41: #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 09:52:41: #1 tags after filtering in treatment: 13788709 INFO @ Tue, 16 Jun 2020 09:52:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:52:41: #1 finished! INFO @ Tue, 16 Jun 2020 09:52:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:52:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:52:42: #2 number of paired peaks: 267 WARNING @ Tue, 16 Jun 2020 09:52:42: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Tue, 16 Jun 2020 09:52:42: start model_add_line... INFO @ Tue, 16 Jun 2020 09:52:42: 8000000 INFO @ Tue, 16 Jun 2020 09:52:42: start X-correlation... INFO @ Tue, 16 Jun 2020 09:52:42: end of X-cor INFO @ Tue, 16 Jun 2020 09:52:42: #2 finished! INFO @ Tue, 16 Jun 2020 09:52:42: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:52:42: #2 alternative fragment length(s) may be 2,50 bps INFO @ Tue, 16 Jun 2020 09:52:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982105/SRX982105.05_model.r WARNING @ Tue, 16 Jun 2020 09:52:42: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:52:42: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Tue, 16 Jun 2020 09:52:42: #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 09:52:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:52:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:52:47: 3000000 INFO @ Tue, 16 Jun 2020 09:52:48: 9000000 INFO @ Tue, 16 Jun 2020 09:52:53: 10000000 INFO @ Tue, 16 Jun 2020 09:52:54: 4000000 INFO @ Tue, 16 Jun 2020 09:52:59: 11000000 INFO @ Tue, 16 Jun 2020 09:53:01: 5000000 INFO @ Tue, 16 Jun 2020 09:53:05: 12000000 INFO @ Tue, 16 Jun 2020 09:53:08: 6000000 INFO @ Tue, 16 Jun 2020 09:53:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:53:11: 13000000 INFO @ Tue, 16 Jun 2020 09:53:15: 7000000 INFO @ Tue, 16 Jun 2020 09:53:15: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:53:15: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:53:15: #1 total tags in treatment: 13788709 INFO @ Tue, 16 Jun 2020 09:53:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:53:15: #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 09:53:15: #1 tags after filtering in treatment: 13788709 INFO @ Tue, 16 Jun 2020 09:53:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:53:15: #1 finished! INFO @ Tue, 16 Jun 2020 09:53:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:53:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:53:16: #2 number of paired peaks: 267 WARNING @ Tue, 16 Jun 2020 09:53:16: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Tue, 16 Jun 2020 09:53:16: start model_add_line... INFO @ Tue, 16 Jun 2020 09:53:16: start X-correlation... INFO @ Tue, 16 Jun 2020 09:53:16: end of X-cor INFO @ Tue, 16 Jun 2020 09:53:16: #2 finished! INFO @ Tue, 16 Jun 2020 09:53:16: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:53:16: #2 alternative fragment length(s) may be 2,50 bps INFO @ Tue, 16 Jun 2020 09:53:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982105/SRX982105.10_model.r WARNING @ Tue, 16 Jun 2020 09:53:16: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:53:16: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Tue, 16 Jun 2020 09:53:16: #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 09:53:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:53:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:53:21: 8000000 INFO @ Tue, 16 Jun 2020 09:53:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982105/SRX982105.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:53:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982105/SRX982105.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:53:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982105/SRX982105.05_summits.bed INFO @ Tue, 16 Jun 2020 09:53:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (650 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:53:28: 9000000 INFO @ Tue, 16 Jun 2020 09:53:34: 10000000 INFO @ Tue, 16 Jun 2020 09:53:40: 11000000 INFO @ Tue, 16 Jun 2020 09:53:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:53:46: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:53:52: 13000000 INFO @ Tue, 16 Jun 2020 09:53:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982105/SRX982105.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:53:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982105/SRX982105.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:53:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982105/SRX982105.10_summits.bed INFO @ Tue, 16 Jun 2020 09:53:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (422 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:53:57: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:53:57: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:53:57: #1 total tags in treatment: 13788709 INFO @ Tue, 16 Jun 2020 09:53:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:53:57: #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 09:53:57: #1 tags after filtering in treatment: 13788709 INFO @ Tue, 16 Jun 2020 09:53:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:53:57: #1 finished! INFO @ Tue, 16 Jun 2020 09:53:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:53:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:53:58: #2 number of paired peaks: 267 WARNING @ Tue, 16 Jun 2020 09:53:58: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Tue, 16 Jun 2020 09:53:58: start model_add_line... INFO @ Tue, 16 Jun 2020 09:53:58: start X-correlation... INFO @ Tue, 16 Jun 2020 09:53:58: end of X-cor INFO @ Tue, 16 Jun 2020 09:53:58: #2 finished! INFO @ Tue, 16 Jun 2020 09:53:58: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:53:58: #2 alternative fragment length(s) may be 2,50 bps INFO @ Tue, 16 Jun 2020 09:53:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982105/SRX982105.20_model.r WARNING @ Tue, 16 Jun 2020 09:53:58: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:53:58: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Tue, 16 Jun 2020 09:53:58: #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 09:53:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:53:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:54:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:54:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982105/SRX982105.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:54:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982105/SRX982105.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:54:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982105/SRX982105.20_summits.bed INFO @ Tue, 16 Jun 2020 09:54:37: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (177 records, 4 fields): 1 millis CompletedMACS2peakCalling