Job ID = 6366842 SRX = SRX2350741 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:10:16 prefetch.2.10.7: 1) Downloading 'SRR5024050'... 2020-06-15T23:10:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:12:08 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:12:09 prefetch.2.10.7: 'SRR5024050' is valid 2020-06-15T23:12:09 prefetch.2.10.7: 1) 'SRR5024050' was downloaded successfully Read 10864382 spots for SRR5024050/SRR5024050.sra Written 10864382 spots for SRR5024050/SRR5024050.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: 00:02:23 10864382 reads; of these: 10864382 (100.00%) were unpaired; of these: 536173 (4.94%) aligned 0 times 8994471 (82.79%) aligned exactly 1 time 1333738 (12.28%) aligned >1 times 95.06% overall alignment rate Time searching: 00:02:23 Overall time: 00:02:23 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] 646756 / 10328209 = 0.0626 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 08:17:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350741/SRX2350741.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350741/SRX2350741.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350741/SRX2350741.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350741/SRX2350741.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 08:17:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:17:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:18:03: 1000000 INFO @ Tue, 16 Jun 2020 08:18:09: 2000000 INFO @ Tue, 16 Jun 2020 08:18:15: 3000000 INFO @ Tue, 16 Jun 2020 08:18:21: 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 08:18:27: 5000000 INFO @ Tue, 16 Jun 2020 08:18:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350741/SRX2350741.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350741/SRX2350741.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350741/SRX2350741.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350741/SRX2350741.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 08:18:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:18:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:18:33: 6000000 INFO @ Tue, 16 Jun 2020 08:18:35: 1000000 INFO @ Tue, 16 Jun 2020 08:18:40: 7000000 INFO @ Tue, 16 Jun 2020 08:18:43: 2000000 INFO @ Tue, 16 Jun 2020 08:18:47: 8000000 INFO @ Tue, 16 Jun 2020 08:18:50: 3000000 INFO @ Tue, 16 Jun 2020 08:18:54: 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 08:18:57: 4000000 INFO @ Tue, 16 Jun 2020 08:18:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350741/SRX2350741.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350741/SRX2350741.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350741/SRX2350741.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350741/SRX2350741.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 08:18:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:18:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:18:59: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:18:59: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:18:59: #1 total tags in treatment: 9681453 INFO @ Tue, 16 Jun 2020 08:18:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:18:59: #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 08:18:59: #1 tags after filtering in treatment: 9681453 INFO @ Tue, 16 Jun 2020 08:18:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:18:59: #1 finished! INFO @ Tue, 16 Jun 2020 08:18:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:18:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:19:00: #2 number of paired peaks: 219 WARNING @ Tue, 16 Jun 2020 08:19:00: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Tue, 16 Jun 2020 08:19:00: start model_add_line... INFO @ Tue, 16 Jun 2020 08:19:00: start X-correlation... INFO @ Tue, 16 Jun 2020 08:19:00: end of X-cor INFO @ Tue, 16 Jun 2020 08:19:00: #2 finished! INFO @ Tue, 16 Jun 2020 08:19:00: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:19:00: #2 alternative fragment length(s) may be 3,49 bps INFO @ Tue, 16 Jun 2020 08:19:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350741/SRX2350741.05_model.r WARNING @ Tue, 16 Jun 2020 08:19:00: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:19:00: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Tue, 16 Jun 2020 08:19:00: #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 08:19:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:19:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:19:05: 1000000 INFO @ Tue, 16 Jun 2020 08:19:05: 5000000 INFO @ Tue, 16 Jun 2020 08:19:12: 2000000 INFO @ Tue, 16 Jun 2020 08:19:12: 6000000 INFO @ Tue, 16 Jun 2020 08:19:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:19:18: 3000000 INFO @ Tue, 16 Jun 2020 08:19:19: 7000000 INFO @ Tue, 16 Jun 2020 08:19:25: 4000000 INFO @ Tue, 16 Jun 2020 08:19:27: 8000000 INFO @ Tue, 16 Jun 2020 08:19:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350741/SRX2350741.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:19:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350741/SRX2350741.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:19:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350741/SRX2350741.05_summits.bed INFO @ Tue, 16 Jun 2020 08:19:28: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (480 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:19:32: 5000000 INFO @ Tue, 16 Jun 2020 08:19:34: 9000000 INFO @ Tue, 16 Jun 2020 08:19:39: 6000000 INFO @ Tue, 16 Jun 2020 08:19:39: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:19:39: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:19:39: #1 total tags in treatment: 9681453 INFO @ Tue, 16 Jun 2020 08:19:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:19:39: #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 08:19:39: #1 tags after filtering in treatment: 9681453 INFO @ Tue, 16 Jun 2020 08:19:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:19:39: #1 finished! INFO @ Tue, 16 Jun 2020 08:19:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:19:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:19:40: #2 number of paired peaks: 219 WARNING @ Tue, 16 Jun 2020 08:19:40: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Tue, 16 Jun 2020 08:19:40: start model_add_line... INFO @ Tue, 16 Jun 2020 08:19:40: start X-correlation... INFO @ Tue, 16 Jun 2020 08:19:40: end of X-cor INFO @ Tue, 16 Jun 2020 08:19:40: #2 finished! INFO @ Tue, 16 Jun 2020 08:19:40: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:19:40: #2 alternative fragment length(s) may be 3,49 bps INFO @ Tue, 16 Jun 2020 08:19:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350741/SRX2350741.10_model.r WARNING @ Tue, 16 Jun 2020 08:19:40: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:19:40: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Tue, 16 Jun 2020 08:19:40: #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 08:19:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:19:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:19:45: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:19:52: 8000000 INFO @ Tue, 16 Jun 2020 08:19:57: 9000000 INFO @ Tue, 16 Jun 2020 08:19:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:20:02: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:20:02: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:20:02: #1 total tags in treatment: 9681453 INFO @ Tue, 16 Jun 2020 08:20:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:20:02: #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 08:20:02: #1 tags after filtering in treatment: 9681453 INFO @ Tue, 16 Jun 2020 08:20:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:20:02: #1 finished! INFO @ Tue, 16 Jun 2020 08:20:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:20:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:20:03: #2 number of paired peaks: 219 WARNING @ Tue, 16 Jun 2020 08:20:03: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Tue, 16 Jun 2020 08:20:03: start model_add_line... INFO @ Tue, 16 Jun 2020 08:20:03: start X-correlation... INFO @ Tue, 16 Jun 2020 08:20:03: end of X-cor INFO @ Tue, 16 Jun 2020 08:20:03: #2 finished! INFO @ Tue, 16 Jun 2020 08:20:03: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 08:20:03: #2 alternative fragment length(s) may be 3,49 bps INFO @ Tue, 16 Jun 2020 08:20:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350741/SRX2350741.20_model.r WARNING @ Tue, 16 Jun 2020 08:20:03: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:20:03: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Tue, 16 Jun 2020 08:20:03: #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 08:20:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:20:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:20:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350741/SRX2350741.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:20:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350741/SRX2350741.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:20:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350741/SRX2350741.10_summits.bed INFO @ Tue, 16 Jun 2020 08:20:09: Done! BigWig に変換しました。 pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (257 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:20:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:20:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350741/SRX2350741.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:20:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350741/SRX2350741.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:20:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350741/SRX2350741.20_summits.bed INFO @ Tue, 16 Jun 2020 08:20:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (106 records, 4 fields): 1 millis CompletedMACS2peakCalling