Job ID = 6367983 SRX = SRX4626835 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:44:29 prefetch.2.10.7: 1) Downloading 'SRR7771418'... 2020-06-15T23:44:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:46:06 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:46:06 prefetch.2.10.7: 'SRR7771418' is valid 2020-06-15T23:46:06 prefetch.2.10.7: 1) 'SRR7771418' was downloaded successfully Read 12433035 spots for SRR7771418/SRR7771418.sra Written 12433035 spots for SRR7771418/SRR7771418.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: 00:02:14 12433035 reads; of these: 12433035 (100.00%) were unpaired; of these: 907942 (7.30%) aligned 0 times 9734677 (78.30%) aligned exactly 1 time 1790416 (14.40%) aligned >1 times 92.70% overall alignment rate Time searching: 00:02:14 Overall time: 00:02:14 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_rmdupse_core] 5429612 / 11525093 = 0.4711 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 08:51:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4626835/SRX4626835.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4626835/SRX4626835.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4626835/SRX4626835.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4626835/SRX4626835.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 08:51:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:51:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:51:15: 1000000 INFO @ Tue, 16 Jun 2020 08:51:19: 2000000 INFO @ Tue, 16 Jun 2020 08:51:24: 3000000 INFO @ Tue, 16 Jun 2020 08:51:29: 4000000 INFO @ Tue, 16 Jun 2020 08:51:33: 5000000 INFO @ Tue, 16 Jun 2020 08:51:38: 6000000 INFO @ Tue, 16 Jun 2020 08:51:38: #1 tag size is determined as 40 bps INFO @ Tue, 16 Jun 2020 08:51:38: #1 tag size = 40 INFO @ Tue, 16 Jun 2020 08:51:38: #1 total tags in treatment: 6095481 INFO @ Tue, 16 Jun 2020 08:51:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:51:38: #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 08:51:38: #1 tags after filtering in treatment: 6095481 INFO @ Tue, 16 Jun 2020 08:51:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:51:38: #1 finished! INFO @ Tue, 16 Jun 2020 08:51:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:51:38: #2 looking for paired plus/minus strand peaks... 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 08:51:39: #2 number of paired peaks: 508 WARNING @ Tue, 16 Jun 2020 08:51:39: Fewer paired peaks (508) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 508 pairs to build model! INFO @ Tue, 16 Jun 2020 08:51:39: start model_add_line... INFO @ Tue, 16 Jun 2020 08:51:39: start X-correlation... INFO @ Tue, 16 Jun 2020 08:51:39: end of X-cor INFO @ Tue, 16 Jun 2020 08:51:39: #2 finished! INFO @ Tue, 16 Jun 2020 08:51:39: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 08:51:39: #2 alternative fragment length(s) may be 4,50 bps INFO @ Tue, 16 Jun 2020 08:51:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4626835/SRX4626835.05_model.r WARNING @ Tue, 16 Jun 2020 08:51:39: #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 08:51:39: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Tue, 16 Jun 2020 08:51:39: #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 08:51:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:51:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:51:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4626835/SRX4626835.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4626835/SRX4626835.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4626835/SRX4626835.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4626835/SRX4626835.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 08:51:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:51:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:51:45: 1000000 INFO @ Tue, 16 Jun 2020 08:51:49: 2000000 INFO @ Tue, 16 Jun 2020 08:51:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:51:54: 3000000 INFO @ Tue, 16 Jun 2020 08:51:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4626835/SRX4626835.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:51:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4626835/SRX4626835.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:51:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4626835/SRX4626835.05_summits.bed INFO @ Tue, 16 Jun 2020 08:51:57: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (949 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:51:59: 4000000 INFO @ Tue, 16 Jun 2020 08:52:03: 5000000 INFO @ Tue, 16 Jun 2020 08:52:08: 6000000 INFO @ Tue, 16 Jun 2020 08:52:08: #1 tag size is determined as 40 bps INFO @ Tue, 16 Jun 2020 08:52:08: #1 tag size = 40 INFO @ Tue, 16 Jun 2020 08:52:08: #1 total tags in treatment: 6095481 INFO @ Tue, 16 Jun 2020 08:52:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:52:08: #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 08:52:08: #1 tags after filtering in treatment: 6095481 INFO @ Tue, 16 Jun 2020 08:52:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:52:08: #1 finished! INFO @ Tue, 16 Jun 2020 08:52:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:52:08: #2 looking for paired plus/minus strand peaks... 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 08:52:09: #2 number of paired peaks: 508 WARNING @ Tue, 16 Jun 2020 08:52:09: Fewer paired peaks (508) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 508 pairs to build model! INFO @ Tue, 16 Jun 2020 08:52:09: start model_add_line... INFO @ Tue, 16 Jun 2020 08:52:09: start X-correlation... INFO @ Tue, 16 Jun 2020 08:52:09: end of X-cor INFO @ Tue, 16 Jun 2020 08:52:09: #2 finished! INFO @ Tue, 16 Jun 2020 08:52:09: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 08:52:09: #2 alternative fragment length(s) may be 4,50 bps INFO @ Tue, 16 Jun 2020 08:52:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4626835/SRX4626835.10_model.r WARNING @ Tue, 16 Jun 2020 08:52:09: #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 08:52:09: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Tue, 16 Jun 2020 08:52:09: #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 08:52:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:52:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:52:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4626835/SRX4626835.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4626835/SRX4626835.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4626835/SRX4626835.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4626835/SRX4626835.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 08:52:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:52:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:52:15: 1000000 INFO @ Tue, 16 Jun 2020 08:52:20: 2000000 INFO @ Tue, 16 Jun 2020 08:52:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:52:24: 3000000 INFO @ Tue, 16 Jun 2020 08:52:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4626835/SRX4626835.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:52:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4626835/SRX4626835.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:52:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4626835/SRX4626835.10_summits.bed INFO @ Tue, 16 Jun 2020 08:52:28: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (449 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:52:29: 4000000 INFO @ Tue, 16 Jun 2020 08:52:34: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:52:38: 6000000 INFO @ Tue, 16 Jun 2020 08:52:39: #1 tag size is determined as 40 bps INFO @ Tue, 16 Jun 2020 08:52:39: #1 tag size = 40 INFO @ Tue, 16 Jun 2020 08:52:39: #1 total tags in treatment: 6095481 INFO @ Tue, 16 Jun 2020 08:52:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:52:39: #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 08:52:39: #1 tags after filtering in treatment: 6095481 INFO @ Tue, 16 Jun 2020 08:52:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:52:39: #1 finished! INFO @ Tue, 16 Jun 2020 08:52:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:52:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:52:39: #2 number of paired peaks: 508 WARNING @ Tue, 16 Jun 2020 08:52:39: Fewer paired peaks (508) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 508 pairs to build model! INFO @ Tue, 16 Jun 2020 08:52:39: start model_add_line... INFO @ Tue, 16 Jun 2020 08:52:40: start X-correlation... INFO @ Tue, 16 Jun 2020 08:52:40: end of X-cor INFO @ Tue, 16 Jun 2020 08:52:40: #2 finished! INFO @ Tue, 16 Jun 2020 08:52:40: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 08:52:40: #2 alternative fragment length(s) may be 4,50 bps INFO @ Tue, 16 Jun 2020 08:52:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4626835/SRX4626835.20_model.r WARNING @ Tue, 16 Jun 2020 08:52:40: #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 08:52:40: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Tue, 16 Jun 2020 08:52:40: #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 08:52:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:52:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:52:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:52:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4626835/SRX4626835.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:52:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4626835/SRX4626835.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:52:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4626835/SRX4626835.20_summits.bed INFO @ Tue, 16 Jun 2020 08:52:59: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (156 records, 4 fields): 1 millis CompletedMACS2peakCalling