Job ID = 6367694 SRX = SRX3942557 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:32:05 prefetch.2.10.7: 1) Downloading 'SRR7010078'... 2020-06-15T23:32:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:34:54 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:34:55 prefetch.2.10.7: 'SRR7010078' is valid 2020-06-15T23:34:55 prefetch.2.10.7: 1) 'SRR7010078' was downloaded successfully 2020-06-15T23:34:55 prefetch.2.10.7: 'SRR7010078' has 0 unresolved dependencies Read 17425224 spots for SRR7010078/SRR7010078.sra Written 17425224 spots for SRR7010078/SRR7010078.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: 00:06:41 17425224 reads; of these: 17425224 (100.00%) were unpaired; of these: 1376217 (7.90%) aligned 0 times 12856257 (73.78%) aligned exactly 1 time 3192750 (18.32%) aligned >1 times 92.10% overall alignment rate Time searching: 00:06:41 Overall time: 00:06:41 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] 3621252 / 16049007 = 0.2256 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 08:48:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3942557/SRX3942557.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3942557/SRX3942557.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3942557/SRX3942557.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3942557/SRX3942557.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 08:48:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:48:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:48:12: 1000000 INFO @ Tue, 16 Jun 2020 08:48:17: 2000000 INFO @ Tue, 16 Jun 2020 08:48:23: 3000000 INFO @ Tue, 16 Jun 2020 08:48:28: 4000000 INFO @ Tue, 16 Jun 2020 08:48:34: 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 08:48:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3942557/SRX3942557.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3942557/SRX3942557.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3942557/SRX3942557.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3942557/SRX3942557.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 08:48:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:48:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:48:40: 6000000 INFO @ Tue, 16 Jun 2020 08:48:43: 1000000 INFO @ Tue, 16 Jun 2020 08:48:46: 7000000 INFO @ Tue, 16 Jun 2020 08:48:49: 2000000 INFO @ Tue, 16 Jun 2020 08:48:52: 8000000 INFO @ Tue, 16 Jun 2020 08:48:55: 3000000 INFO @ Tue, 16 Jun 2020 08:48:58: 9000000 INFO @ Tue, 16 Jun 2020 08:49:02: 4000000 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 08:49:04: 10000000 INFO @ Tue, 16 Jun 2020 08:49:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3942557/SRX3942557.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3942557/SRX3942557.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3942557/SRX3942557.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3942557/SRX3942557.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 08:49:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:49:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:49:09: 5000000 INFO @ Tue, 16 Jun 2020 08:49:11: 11000000 INFO @ Tue, 16 Jun 2020 08:49:14: 1000000 INFO @ Tue, 16 Jun 2020 08:49:16: 6000000 INFO @ Tue, 16 Jun 2020 08:49:18: 12000000 INFO @ Tue, 16 Jun 2020 08:49:21: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:49:21: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:49:21: #1 total tags in treatment: 12427755 INFO @ Tue, 16 Jun 2020 08:49:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:49:21: #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 08:49:22: #1 tags after filtering in treatment: 12427755 INFO @ Tue, 16 Jun 2020 08:49:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:49:22: #1 finished! INFO @ Tue, 16 Jun 2020 08:49:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:49:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:49:22: 2000000 INFO @ Tue, 16 Jun 2020 08:49:23: #2 number of paired peaks: 438 WARNING @ Tue, 16 Jun 2020 08:49:23: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Tue, 16 Jun 2020 08:49:23: start model_add_line... INFO @ Tue, 16 Jun 2020 08:49:23: start X-correlation... INFO @ Tue, 16 Jun 2020 08:49:23: end of X-cor INFO @ Tue, 16 Jun 2020 08:49:23: #2 finished! INFO @ Tue, 16 Jun 2020 08:49:23: #2 predicted fragment length is 66 bps INFO @ Tue, 16 Jun 2020 08:49:23: #2 alternative fragment length(s) may be 2,66,561 bps INFO @ Tue, 16 Jun 2020 08:49:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3942557/SRX3942557.05_model.r WARNING @ Tue, 16 Jun 2020 08:49:23: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:49:23: #2 You may need to consider one of the other alternative d(s): 2,66,561 WARNING @ Tue, 16 Jun 2020 08:49:23: #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 08:49:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:49:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:49:23: 7000000 INFO @ Tue, 16 Jun 2020 08:49:29: 3000000 INFO @ Tue, 16 Jun 2020 08:49:30: 8000000 INFO @ Tue, 16 Jun 2020 08:49:36: 4000000 INFO @ Tue, 16 Jun 2020 08:49:36: 9000000 INFO @ Tue, 16 Jun 2020 08:49:42: 5000000 INFO @ Tue, 16 Jun 2020 08:49:43: 10000000 INFO @ Tue, 16 Jun 2020 08:49:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:49:49: 6000000 INFO @ Tue, 16 Jun 2020 08:49:49: 11000000 INFO @ Tue, 16 Jun 2020 08:49:55: 7000000 INFO @ Tue, 16 Jun 2020 08:49:56: 12000000 INFO @ Tue, 16 Jun 2020 08:49:59: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:49:59: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:49:59: #1 total tags in treatment: 12427755 INFO @ Tue, 16 Jun 2020 08:49:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:49:59: #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 08:49:59: #1 tags after filtering in treatment: 12427755 INFO @ Tue, 16 Jun 2020 08:49:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:49:59: #1 finished! INFO @ Tue, 16 Jun 2020 08:49:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:49:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3942557/SRX3942557.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:50:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3942557/SRX3942557.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:50:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3942557/SRX3942557.05_summits.bed INFO @ Tue, 16 Jun 2020 08:50:00: Done! INFO @ Tue, 16 Jun 2020 08:50:00: #2 number of paired peaks: 438 WARNING @ Tue, 16 Jun 2020 08:50:00: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Tue, 16 Jun 2020 08:50:00: start model_add_line... pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3440 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:50:00: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:00: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:00: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:00: #2 predicted fragment length is 66 bps INFO @ Tue, 16 Jun 2020 08:50:00: #2 alternative fragment length(s) may be 2,66,561 bps INFO @ Tue, 16 Jun 2020 08:50:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3942557/SRX3942557.10_model.r WARNING @ Tue, 16 Jun 2020 08:50:00: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:50:00: #2 You may need to consider one of the other alternative d(s): 2,66,561 WARNING @ Tue, 16 Jun 2020 08:50:00: #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 08:50:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:50:02: 8000000 INFO @ Tue, 16 Jun 2020 08:50:08: 9000000 INFO @ Tue, 16 Jun 2020 08:50:13: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:50:19: 11000000 INFO @ Tue, 16 Jun 2020 08:50:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:50:25: 12000000 INFO @ Tue, 16 Jun 2020 08:50:27: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 08:50:27: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 08:50:27: #1 total tags in treatment: 12427755 INFO @ Tue, 16 Jun 2020 08:50:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:27: #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 08:50:27: #1 tags after filtering in treatment: 12427755 INFO @ Tue, 16 Jun 2020 08:50:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:50:27: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:28: #2 number of paired peaks: 438 WARNING @ Tue, 16 Jun 2020 08:50:28: Fewer paired peaks (438) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 438 pairs to build model! INFO @ Tue, 16 Jun 2020 08:50:28: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:28: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:28: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:28: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:28: #2 predicted fragment length is 66 bps INFO @ Tue, 16 Jun 2020 08:50:28: #2 alternative fragment length(s) may be 2,66,561 bps INFO @ Tue, 16 Jun 2020 08:50:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3942557/SRX3942557.20_model.r WARNING @ Tue, 16 Jun 2020 08:50:28: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:50:28: #2 You may need to consider one of the other alternative d(s): 2,66,561 WARNING @ Tue, 16 Jun 2020 08:50:28: #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 08:50:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:50:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3942557/SRX3942557.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:50:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3942557/SRX3942557.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:50:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3942557/SRX3942557.10_summits.bed INFO @ Tue, 16 Jun 2020 08:50:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (792 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:50:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:51:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3942557/SRX3942557.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:51:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3942557/SRX3942557.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:51:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3942557/SRX3942557.20_summits.bed INFO @ Tue, 16 Jun 2020 08:51:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (205 records, 4 fields): 1 millis CompletedMACS2peakCalling