Job ID = 6367218 SRX = SRX3043404 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:26:21 prefetch.2.10.7: 1) Downloading 'SRR5875888'... 2020-06-15T23:26:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:28:06 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:28:07 prefetch.2.10.7: 'SRR5875888' is valid 2020-06-15T23:28:07 prefetch.2.10.7: 1) 'SRR5875888' was downloaded successfully Read 11272212 spots for SRR5875888/SRR5875888.sra Written 11272212 spots for SRR5875888/SRR5875888.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: 00:03:09 11272212 reads; of these: 11272212 (100.00%) were unpaired; of these: 211990 (1.88%) aligned 0 times 9634662 (85.47%) aligned exactly 1 time 1425560 (12.65%) aligned >1 times 98.12% overall alignment rate Time searching: 00:03:09 Overall time: 00:03:09 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] 1135243 / 11060222 = 0.1026 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 08:35:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043404/SRX3043404.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043404/SRX3043404.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043404/SRX3043404.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043404/SRX3043404.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 08:35:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:35:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:35:33: 1000000 INFO @ Tue, 16 Jun 2020 08:35:39: 2000000 INFO @ Tue, 16 Jun 2020 08:35:45: 3000000 INFO @ Tue, 16 Jun 2020 08:35:52: 4000000 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 08:35:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043404/SRX3043404.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043404/SRX3043404.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043404/SRX3043404.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043404/SRX3043404.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 08:35:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:35:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:35:58: 5000000 INFO @ Tue, 16 Jun 2020 08:36:03: 1000000 INFO @ Tue, 16 Jun 2020 08:36:04: 6000000 INFO @ Tue, 16 Jun 2020 08:36:09: 2000000 INFO @ Tue, 16 Jun 2020 08:36:11: 7000000 INFO @ Tue, 16 Jun 2020 08:36:16: 3000000 INFO @ Tue, 16 Jun 2020 08:36:17: 8000000 INFO @ Tue, 16 Jun 2020 08:36:22: 4000000 INFO @ Tue, 16 Jun 2020 08:36:24: 9000000 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 08:36:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043404/SRX3043404.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043404/SRX3043404.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043404/SRX3043404.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043404/SRX3043404.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 08:36:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:36:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:36:28: 5000000 INFO @ Tue, 16 Jun 2020 08:36:30: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:36:30: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:36:30: #1 total tags in treatment: 9924979 INFO @ Tue, 16 Jun 2020 08:36:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:36:30: #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 08:36:30: #1 tags after filtering in treatment: 9924979 INFO @ Tue, 16 Jun 2020 08:36:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:36:30: #1 finished! INFO @ Tue, 16 Jun 2020 08:36:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:36:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:36:31: #2 number of paired peaks: 164 WARNING @ Tue, 16 Jun 2020 08:36:31: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Tue, 16 Jun 2020 08:36:31: start model_add_line... INFO @ Tue, 16 Jun 2020 08:36:31: start X-correlation... INFO @ Tue, 16 Jun 2020 08:36:31: end of X-cor INFO @ Tue, 16 Jun 2020 08:36:31: #2 finished! INFO @ Tue, 16 Jun 2020 08:36:31: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 08:36:31: #2 alternative fragment length(s) may be 3,50,472,589,596 bps INFO @ Tue, 16 Jun 2020 08:36:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043404/SRX3043404.05_model.r WARNING @ Tue, 16 Jun 2020 08:36:31: #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 08:36:31: #2 You may need to consider one of the other alternative d(s): 3,50,472,589,596 WARNING @ Tue, 16 Jun 2020 08:36:31: #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 08:36:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:36:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:36:33: 1000000 INFO @ Tue, 16 Jun 2020 08:36:34: 6000000 INFO @ Tue, 16 Jun 2020 08:36:39: 2000000 INFO @ Tue, 16 Jun 2020 08:36:41: 7000000 INFO @ Tue, 16 Jun 2020 08:36:46: 3000000 INFO @ Tue, 16 Jun 2020 08:36:47: 8000000 INFO @ Tue, 16 Jun 2020 08:36:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:36:52: 4000000 INFO @ Tue, 16 Jun 2020 08:36:53: 9000000 INFO @ Tue, 16 Jun 2020 08:36:58: 5000000 INFO @ Tue, 16 Jun 2020 08:36:59: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:36:59: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:36:59: #1 total tags in treatment: 9924979 INFO @ Tue, 16 Jun 2020 08:36:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:36:59: #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 08:36:59: #1 tags after filtering in treatment: 9924979 INFO @ Tue, 16 Jun 2020 08:36:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:36:59: #1 finished! INFO @ Tue, 16 Jun 2020 08:36:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:36:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:36:59: #2 number of paired peaks: 164 WARNING @ Tue, 16 Jun 2020 08:36:59: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Tue, 16 Jun 2020 08:36:59: start model_add_line... INFO @ Tue, 16 Jun 2020 08:37:00: start X-correlation... INFO @ Tue, 16 Jun 2020 08:37:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3043404/SRX3043404.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:00: end of X-cor INFO @ Tue, 16 Jun 2020 08:37:00: #2 finished! INFO @ Tue, 16 Jun 2020 08:37:00: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 08:37:00: #2 alternative fragment length(s) may be 3,50,472,589,596 bps INFO @ Tue, 16 Jun 2020 08:37:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043404/SRX3043404.10_model.r WARNING @ Tue, 16 Jun 2020 08:37:00: #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 08:37:00: #2 You may need to consider one of the other alternative d(s): 3,50,472,589,596 WARNING @ Tue, 16 Jun 2020 08:37:00: #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 08:37:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:37:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:37:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3043404/SRX3043404.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3043404/SRX3043404.05_summits.bed INFO @ Tue, 16 Jun 2020 08:37:00: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1434 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:37:04: 6000000 INFO @ Tue, 16 Jun 2020 08:37:10: 7000000 INFO @ Tue, 16 Jun 2020 08:37:16: 8000000 INFO @ Tue, 16 Jun 2020 08:37:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:37:22: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:37:28: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:37:28: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:37:28: #1 total tags in treatment: 9924979 INFO @ Tue, 16 Jun 2020 08:37:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:37:28: #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 08:37:28: #1 tags after filtering in treatment: 9924979 INFO @ Tue, 16 Jun 2020 08:37:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:37:28: #1 finished! INFO @ Tue, 16 Jun 2020 08:37:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:37:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:37:29: #2 number of paired peaks: 164 WARNING @ Tue, 16 Jun 2020 08:37:29: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Tue, 16 Jun 2020 08:37:29: start model_add_line... INFO @ Tue, 16 Jun 2020 08:37:29: start X-correlation... INFO @ Tue, 16 Jun 2020 08:37:29: end of X-cor INFO @ Tue, 16 Jun 2020 08:37:29: #2 finished! INFO @ Tue, 16 Jun 2020 08:37:29: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 08:37:29: #2 alternative fragment length(s) may be 3,50,472,589,596 bps INFO @ Tue, 16 Jun 2020 08:37:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043404/SRX3043404.20_model.r WARNING @ Tue, 16 Jun 2020 08:37:29: #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 08:37:29: #2 You may need to consider one of the other alternative d(s): 3,50,472,589,596 WARNING @ Tue, 16 Jun 2020 08:37:29: #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 08:37:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:37:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:37:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3043404/SRX3043404.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3043404/SRX3043404.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3043404/SRX3043404.10_summits.bed INFO @ Tue, 16 Jun 2020 08:37:30: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (302 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:37:48: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:37:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3043404/SRX3043404.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:37:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3043404/SRX3043404.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:37:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3043404/SRX3043404.20_summits.bed INFO @ Tue, 16 Jun 2020 08:37:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (93 records, 4 fields): 1 millis CompletedMACS2peakCalling