Job ID = 6369047 SRX = SRX982111 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:44:54 prefetch.2.10.7: 1) Downloading 'SRR1956601'... 2020-06-16T00:44:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:46:57 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:46:58 prefetch.2.10.7: 'SRR1956601' is valid 2020-06-16T00:46:58 prefetch.2.10.7: 1) 'SRR1956601' was downloaded successfully Read 14118317 spots for SRR1956601/SRR1956601.sra Written 14118317 spots for SRR1956601/SRR1956601.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: 00:02:59 14118317 reads; of these: 14118317 (100.00%) were unpaired; of these: 1984452 (14.06%) aligned 0 times 10203248 (72.27%) aligned exactly 1 time 1930617 (13.67%) aligned >1 times 85.94% overall alignment rate Time searching: 00:02:59 Overall time: 00:02:59 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] 898524 / 12133865 = 0.0741 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 09:54:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982111/SRX982111.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982111/SRX982111.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982111/SRX982111.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982111/SRX982111.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 09:54:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:54:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:55:06: 1000000 INFO @ Tue, 16 Jun 2020 09:55:13: 2000000 INFO @ Tue, 16 Jun 2020 09:55:21: 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 @ Tue, 16 Jun 2020 09:55:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982111/SRX982111.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982111/SRX982111.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982111/SRX982111.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982111/SRX982111.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 09:55:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:55:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:55:29: 4000000 INFO @ Tue, 16 Jun 2020 09:55:36: 1000000 INFO @ Tue, 16 Jun 2020 09:55:37: 5000000 INFO @ Tue, 16 Jun 2020 09:55:44: 2000000 INFO @ Tue, 16 Jun 2020 09:55:45: 6000000 INFO @ Tue, 16 Jun 2020 09:55:52: 3000000 INFO @ Tue, 16 Jun 2020 09:55:53: 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 @ Tue, 16 Jun 2020 09:55:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982111/SRX982111.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982111/SRX982111.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982111/SRX982111.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982111/SRX982111.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 09:55:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:55:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:56:00: 4000000 INFO @ Tue, 16 Jun 2020 09:56:02: 8000000 INFO @ Tue, 16 Jun 2020 09:56:08: 1000000 INFO @ Tue, 16 Jun 2020 09:56:08: 5000000 INFO @ Tue, 16 Jun 2020 09:56:10: 9000000 INFO @ Tue, 16 Jun 2020 09:56:16: 2000000 INFO @ Tue, 16 Jun 2020 09:56:17: 6000000 INFO @ Tue, 16 Jun 2020 09:56:18: 10000000 INFO @ Tue, 16 Jun 2020 09:56:25: 3000000 INFO @ Tue, 16 Jun 2020 09:56:25: 7000000 INFO @ Tue, 16 Jun 2020 09:56:26: 11000000 INFO @ Tue, 16 Jun 2020 09:56:28: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:56:28: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:56:28: #1 total tags in treatment: 11235341 INFO @ Tue, 16 Jun 2020 09:56:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:56:28: #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 09:56:28: #1 tags after filtering in treatment: 11235341 INFO @ Tue, 16 Jun 2020 09:56:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:56:28: #1 finished! INFO @ Tue, 16 Jun 2020 09:56:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:56:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:56:29: #2 number of paired peaks: 298 WARNING @ Tue, 16 Jun 2020 09:56:29: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Tue, 16 Jun 2020 09:56:29: start model_add_line... INFO @ Tue, 16 Jun 2020 09:56:29: start X-correlation... INFO @ Tue, 16 Jun 2020 09:56:29: end of X-cor INFO @ Tue, 16 Jun 2020 09:56:29: #2 finished! INFO @ Tue, 16 Jun 2020 09:56:29: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 09:56:29: #2 alternative fragment length(s) may be 4,51 bps INFO @ Tue, 16 Jun 2020 09:56:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982111/SRX982111.05_model.r WARNING @ Tue, 16 Jun 2020 09:56:29: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:56:29: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Tue, 16 Jun 2020 09:56:29: #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 09:56:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:56:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:56:33: 4000000 INFO @ Tue, 16 Jun 2020 09:56:33: 8000000 INFO @ Tue, 16 Jun 2020 09:56:41: 9000000 INFO @ Tue, 16 Jun 2020 09:56:42: 5000000 INFO @ Tue, 16 Jun 2020 09:56:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:56:49: 10000000 INFO @ Tue, 16 Jun 2020 09:56:50: 6000000 INFO @ Tue, 16 Jun 2020 09:56:57: 11000000 INFO @ Tue, 16 Jun 2020 09:56:58: 7000000 INFO @ Tue, 16 Jun 2020 09:56:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982111/SRX982111.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:56:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982111/SRX982111.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:56:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982111/SRX982111.05_summits.bed INFO @ Tue, 16 Jun 2020 09:56:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (592 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:56:59: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:56:59: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:56:59: #1 total tags in treatment: 11235341 INFO @ Tue, 16 Jun 2020 09:56:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:56:59: #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 09:56:59: #1 tags after filtering in treatment: 11235341 INFO @ Tue, 16 Jun 2020 09:56:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:56:59: #1 finished! INFO @ Tue, 16 Jun 2020 09:56:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:56:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:57:00: #2 number of paired peaks: 298 WARNING @ Tue, 16 Jun 2020 09:57:00: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Tue, 16 Jun 2020 09:57:00: start model_add_line... INFO @ Tue, 16 Jun 2020 09:57:00: start X-correlation... INFO @ Tue, 16 Jun 2020 09:57:00: end of X-cor INFO @ Tue, 16 Jun 2020 09:57:00: #2 finished! INFO @ Tue, 16 Jun 2020 09:57:00: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 09:57:00: #2 alternative fragment length(s) may be 4,51 bps INFO @ Tue, 16 Jun 2020 09:57:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982111/SRX982111.10_model.r WARNING @ Tue, 16 Jun 2020 09:57:00: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:57:00: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Tue, 16 Jun 2020 09:57:00: #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 09:57:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:57:00: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:57:06: 8000000 INFO @ Tue, 16 Jun 2020 09:57:14: 9000000 INFO @ Tue, 16 Jun 2020 09:57:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:57:21: 10000000 INFO @ Tue, 16 Jun 2020 09:57:29: 11000000 INFO @ Tue, 16 Jun 2020 09:57:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982111/SRX982111.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:57:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982111/SRX982111.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:57:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982111/SRX982111.10_summits.bed INFO @ Tue, 16 Jun 2020 09:57:31: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (405 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:57:31: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:57:31: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:57:31: #1 total tags in treatment: 11235341 INFO @ Tue, 16 Jun 2020 09:57:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:57:31: #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 09:57:31: #1 tags after filtering in treatment: 11235341 INFO @ Tue, 16 Jun 2020 09:57:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:57:31: #1 finished! INFO @ Tue, 16 Jun 2020 09:57:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:57:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:57:32: #2 number of paired peaks: 298 WARNING @ Tue, 16 Jun 2020 09:57:32: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Tue, 16 Jun 2020 09:57:32: start model_add_line... INFO @ Tue, 16 Jun 2020 09:57:32: start X-correlation... INFO @ Tue, 16 Jun 2020 09:57:32: end of X-cor INFO @ Tue, 16 Jun 2020 09:57:32: #2 finished! INFO @ Tue, 16 Jun 2020 09:57:32: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 09:57:32: #2 alternative fragment length(s) may be 4,51 bps INFO @ Tue, 16 Jun 2020 09:57:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982111/SRX982111.20_model.r WARNING @ Tue, 16 Jun 2020 09:57:32: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:57:32: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Tue, 16 Jun 2020 09:57:32: #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 09:57:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:57:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:57:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:58:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982111/SRX982111.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:58:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982111/SRX982111.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:58:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982111/SRX982111.20_summits.bed INFO @ Tue, 16 Jun 2020 09:58:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (174 records, 4 fields): 1 millis CompletedMACS2peakCalling