Job ID = 6366203 SRX = SRX076078 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:29:44 prefetch.2.10.7: 1) Downloading 'SRR275568'... 2020-06-15T22:29:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:30:32 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:30:33 prefetch.2.10.7: 'SRR275568' is valid 2020-06-15T22:30:33 prefetch.2.10.7: 1) 'SRR275568' was downloaded successfully Read 12676822 spots for SRR275568/SRR275568.sra Written 12676822 spots for SRR275568/SRR275568.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: 00:02:05 12676822 reads; of these: 12676822 (100.00%) were unpaired; of these: 721820 (5.69%) aligned 0 times 9735958 (76.80%) aligned exactly 1 time 2219044 (17.50%) aligned >1 times 94.31% overall alignment rate Time searching: 00:02:05 Overall time: 00:02:05 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] 1316060 / 11955002 = 0.1101 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 07:35:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX076078/SRX076078.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX076078/SRX076078.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX076078/SRX076078.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX076078/SRX076078.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 07:35:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:35:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:35:47: 1000000 INFO @ Tue, 16 Jun 2020 07:35:52: 2000000 INFO @ Tue, 16 Jun 2020 07:35:57: 3000000 INFO @ Tue, 16 Jun 2020 07:36:02: 4000000 INFO @ Tue, 16 Jun 2020 07:36:07: 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 07:36:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX076078/SRX076078.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX076078/SRX076078.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX076078/SRX076078.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX076078/SRX076078.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 07:36:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:36:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:36:11: 6000000 INFO @ Tue, 16 Jun 2020 07:36:16: 1000000 INFO @ Tue, 16 Jun 2020 07:36:17: 7000000 INFO @ Tue, 16 Jun 2020 07:36:21: 2000000 INFO @ Tue, 16 Jun 2020 07:36:22: 8000000 INFO @ Tue, 16 Jun 2020 07:36:26: 3000000 INFO @ Tue, 16 Jun 2020 07:36:27: 9000000 INFO @ Tue, 16 Jun 2020 07:36:31: 4000000 INFO @ Tue, 16 Jun 2020 07:36:32: 10000000 INFO @ Tue, 16 Jun 2020 07:36:36: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:36:36: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:36:36: #1 total tags in treatment: 10638942 INFO @ Tue, 16 Jun 2020 07:36:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:36:36: #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 07:36:36: #1 tags after filtering in treatment: 10638942 INFO @ Tue, 16 Jun 2020 07:36:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:36:36: #1 finished! INFO @ Tue, 16 Jun 2020 07:36:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:36:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:36:36: 5000000 INFO @ Tue, 16 Jun 2020 07:36:36: #2 number of paired peaks: 383 WARNING @ Tue, 16 Jun 2020 07:36:36: Fewer paired peaks (383) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 383 pairs to build model! INFO @ Tue, 16 Jun 2020 07:36:36: start model_add_line... INFO @ Tue, 16 Jun 2020 07:36:37: start X-correlation... INFO @ Tue, 16 Jun 2020 07:36:37: end of X-cor INFO @ Tue, 16 Jun 2020 07:36:37: #2 finished! INFO @ Tue, 16 Jun 2020 07:36:37: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 07:36:37: #2 alternative fragment length(s) may be 1,34,575 bps INFO @ Tue, 16 Jun 2020 07:36:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX076078/SRX076078.05_model.r WARNING @ Tue, 16 Jun 2020 07:36:37: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:36:37: #2 You may need to consider one of the other alternative d(s): 1,34,575 WARNING @ Tue, 16 Jun 2020 07:36:37: #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 07:36:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:36:37: #3 Pre-compute pvalue-qvalue table... 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 07:36:41: 6000000 INFO @ Tue, 16 Jun 2020 07:36:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX076078/SRX076078.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX076078/SRX076078.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX076078/SRX076078.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX076078/SRX076078.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 07:36:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:36:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:36:46: 7000000 INFO @ Tue, 16 Jun 2020 07:36:47: 1000000 INFO @ Tue, 16 Jun 2020 07:36:51: 8000000 INFO @ Tue, 16 Jun 2020 07:36:52: 2000000 INFO @ Tue, 16 Jun 2020 07:36:56: 9000000 INFO @ Tue, 16 Jun 2020 07:36:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:36:58: 3000000 INFO @ Tue, 16 Jun 2020 07:37:01: 10000000 INFO @ Tue, 16 Jun 2020 07:37:04: 4000000 INFO @ Tue, 16 Jun 2020 07:37:04: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:37:04: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:37:04: #1 total tags in treatment: 10638942 INFO @ Tue, 16 Jun 2020 07:37:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:37:04: #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 07:37:04: #1 tags after filtering in treatment: 10638942 INFO @ Tue, 16 Jun 2020 07:37:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:37:04: #1 finished! INFO @ Tue, 16 Jun 2020 07:37:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:37:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:37:05: #2 number of paired peaks: 383 WARNING @ Tue, 16 Jun 2020 07:37:05: Fewer paired peaks (383) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 383 pairs to build model! INFO @ Tue, 16 Jun 2020 07:37:05: start model_add_line... INFO @ Tue, 16 Jun 2020 07:37:05: start X-correlation... INFO @ Tue, 16 Jun 2020 07:37:05: end of X-cor INFO @ Tue, 16 Jun 2020 07:37:05: #2 finished! INFO @ Tue, 16 Jun 2020 07:37:05: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 07:37:05: #2 alternative fragment length(s) may be 1,34,575 bps INFO @ Tue, 16 Jun 2020 07:37:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX076078/SRX076078.10_model.r WARNING @ Tue, 16 Jun 2020 07:37:05: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:37:05: #2 You may need to consider one of the other alternative d(s): 1,34,575 WARNING @ Tue, 16 Jun 2020 07:37:05: #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 07:37:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:37:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:37:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX076078/SRX076078.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:37:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX076078/SRX076078.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:37:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX076078/SRX076078.05_summits.bed INFO @ Tue, 16 Jun 2020 07:37:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (682 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:37:09: 5000000 INFO @ Tue, 16 Jun 2020 07:37:14: 6000000 INFO @ Tue, 16 Jun 2020 07:37:20: 7000000 INFO @ Tue, 16 Jun 2020 07:37:25: 8000000 INFO @ Tue, 16 Jun 2020 07:37:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:37:30: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:37:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX076078/SRX076078.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:37:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX076078/SRX076078.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:37:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX076078/SRX076078.10_summits.bed INFO @ Tue, 16 Jun 2020 07:37:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (298 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:37:35: 10000000 INFO @ Tue, 16 Jun 2020 07:37:39: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 07:37:39: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 07:37:39: #1 total tags in treatment: 10638942 INFO @ Tue, 16 Jun 2020 07:37:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:37:39: #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 07:37:39: #1 tags after filtering in treatment: 10638942 INFO @ Tue, 16 Jun 2020 07:37:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:37:39: #1 finished! INFO @ Tue, 16 Jun 2020 07:37:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:37:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:37:40: #2 number of paired peaks: 383 WARNING @ Tue, 16 Jun 2020 07:37:40: Fewer paired peaks (383) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 383 pairs to build model! INFO @ Tue, 16 Jun 2020 07:37:40: start model_add_line... INFO @ Tue, 16 Jun 2020 07:37:40: start X-correlation... INFO @ Tue, 16 Jun 2020 07:37:40: end of X-cor INFO @ Tue, 16 Jun 2020 07:37:40: #2 finished! INFO @ Tue, 16 Jun 2020 07:37:40: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 07:37:40: #2 alternative fragment length(s) may be 1,34,575 bps INFO @ Tue, 16 Jun 2020 07:37:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX076078/SRX076078.20_model.r WARNING @ Tue, 16 Jun 2020 07:37:40: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:37:40: #2 You may need to consider one of the other alternative d(s): 1,34,575 WARNING @ Tue, 16 Jun 2020 07:37:40: #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 07:37:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:37:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:37:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:38:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX076078/SRX076078.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:38:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX076078/SRX076078.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:38:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX076078/SRX076078.20_summits.bed INFO @ Tue, 16 Jun 2020 07:38:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (97 records, 4 fields): 5 millis CompletedMACS2peakCalling