Job ID = 6507817 SRX = SRX494822 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:26:02 prefetch.2.10.7: 1) Downloading 'SRR1198354'... 2020-06-26T13:26:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:27:15 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:27:16 prefetch.2.10.7: 'SRR1198354' is valid 2020-06-26T13:27:16 prefetch.2.10.7: 1) 'SRR1198354' was downloaded successfully Read 16560194 spots for SRR1198354/SRR1198354.sra Written 16560194 spots for SRR1198354/SRR1198354.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: 00:03:13 16560194 reads; of these: 16560194 (100.00%) were unpaired; of these: 531381 (3.21%) aligned 0 times 13114745 (79.19%) aligned exactly 1 time 2914068 (17.60%) aligned >1 times 96.79% overall alignment rate Time searching: 00:03:13 Overall time: 00:03:13 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] 1976009 / 16028813 = 0.1233 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 @ Fri, 26 Jun 2020 22:36:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494822/SRX494822.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494822/SRX494822.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494822/SRX494822.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494822/SRX494822.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 @ Fri, 26 Jun 2020 22:36:13: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:36:13: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:36:23: 1000000 INFO @ Fri, 26 Jun 2020 22:36:32: 2000000 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 @ Fri, 26 Jun 2020 22:36:41: 3000000 INFO @ Fri, 26 Jun 2020 22:36:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494822/SRX494822.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494822/SRX494822.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494822/SRX494822.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494822/SRX494822.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 @ Fri, 26 Jun 2020 22:36:43: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:36:43: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:36:51: 4000000 INFO @ Fri, 26 Jun 2020 22:36:54: 1000000 INFO @ Fri, 26 Jun 2020 22:37:00: 5000000 INFO @ Fri, 26 Jun 2020 22:37:04: 2000000 INFO @ Fri, 26 Jun 2020 22:37:10: 6000000 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 @ Fri, 26 Jun 2020 22:37:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494822/SRX494822.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494822/SRX494822.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494822/SRX494822.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494822/SRX494822.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 @ Fri, 26 Jun 2020 22:37:13: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:37:13: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:37:14: 3000000 INFO @ Fri, 26 Jun 2020 22:37:19: 7000000 INFO @ Fri, 26 Jun 2020 22:37:24: 1000000 INFO @ Fri, 26 Jun 2020 22:37:24: 4000000 INFO @ Fri, 26 Jun 2020 22:37:29: 8000000 INFO @ Fri, 26 Jun 2020 22:37:34: 2000000 INFO @ Fri, 26 Jun 2020 22:37:35: 5000000 INFO @ Fri, 26 Jun 2020 22:37:38: 9000000 INFO @ Fri, 26 Jun 2020 22:37:44: 3000000 INFO @ Fri, 26 Jun 2020 22:37:45: 6000000 INFO @ Fri, 26 Jun 2020 22:37:48: 10000000 INFO @ Fri, 26 Jun 2020 22:37:55: 4000000 INFO @ Fri, 26 Jun 2020 22:37:55: 7000000 INFO @ Fri, 26 Jun 2020 22:37:57: 11000000 INFO @ Fri, 26 Jun 2020 22:38:05: 5000000 INFO @ Fri, 26 Jun 2020 22:38:06: 8000000 INFO @ Fri, 26 Jun 2020 22:38:07: 12000000 INFO @ Fri, 26 Jun 2020 22:38:16: 6000000 INFO @ Fri, 26 Jun 2020 22:38:16: 9000000 INFO @ Fri, 26 Jun 2020 22:38:16: 13000000 INFO @ Fri, 26 Jun 2020 22:38:26: 14000000 INFO @ Fri, 26 Jun 2020 22:38:26: 7000000 INFO @ Fri, 26 Jun 2020 22:38:26: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:38:26: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:38:26: #1 total tags in treatment: 14052804 INFO @ Fri, 26 Jun 2020 22:38:26: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:38:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:38:26: 10000000 INFO @ Fri, 26 Jun 2020 22:38:27: #1 tags after filtering in treatment: 14052804 INFO @ Fri, 26 Jun 2020 22:38:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:38:27: #1 finished! INFO @ Fri, 26 Jun 2020 22:38:27: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:38:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:38:28: #2 number of paired peaks: 257 WARNING @ Fri, 26 Jun 2020 22:38:28: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Fri, 26 Jun 2020 22:38:28: start model_add_line... INFO @ Fri, 26 Jun 2020 22:38:28: start X-correlation... INFO @ Fri, 26 Jun 2020 22:38:28: end of X-cor INFO @ Fri, 26 Jun 2020 22:38:28: #2 finished! INFO @ Fri, 26 Jun 2020 22:38:28: #2 predicted fragment length is 35 bps INFO @ Fri, 26 Jun 2020 22:38:28: #2 alternative fragment length(s) may be 1,35 bps INFO @ Fri, 26 Jun 2020 22:38:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494822/SRX494822.05_model.r WARNING @ Fri, 26 Jun 2020 22:38:28: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:38:28: #2 You may need to consider one of the other alternative d(s): 1,35 WARNING @ Fri, 26 Jun 2020 22:38:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:38:28: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:38:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:38:36: 8000000 INFO @ Fri, 26 Jun 2020 22:38:37: 11000000 INFO @ Fri, 26 Jun 2020 22:38:46: 9000000 INFO @ Fri, 26 Jun 2020 22:38:47: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:38:53: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:38:57: 10000000 INFO @ Fri, 26 Jun 2020 22:38:57: 13000000 INFO @ Fri, 26 Jun 2020 22:39:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494822/SRX494822.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:39:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494822/SRX494822.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:39:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494822/SRX494822.05_summits.bed INFO @ Fri, 26 Jun 2020 22:39:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1348 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:39:07: 11000000 INFO @ Fri, 26 Jun 2020 22:39:07: 14000000 INFO @ Fri, 26 Jun 2020 22:39:08: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:39:08: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:39:08: #1 total tags in treatment: 14052804 INFO @ Fri, 26 Jun 2020 22:39:08: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:39:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:39:08: #1 tags after filtering in treatment: 14052804 INFO @ Fri, 26 Jun 2020 22:39:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:39:08: #1 finished! INFO @ Fri, 26 Jun 2020 22:39:08: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:39:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:39:09: #2 number of paired peaks: 257 WARNING @ Fri, 26 Jun 2020 22:39:09: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Fri, 26 Jun 2020 22:39:09: start model_add_line... INFO @ Fri, 26 Jun 2020 22:39:09: start X-correlation... INFO @ Fri, 26 Jun 2020 22:39:09: end of X-cor INFO @ Fri, 26 Jun 2020 22:39:09: #2 finished! INFO @ Fri, 26 Jun 2020 22:39:09: #2 predicted fragment length is 35 bps INFO @ Fri, 26 Jun 2020 22:39:09: #2 alternative fragment length(s) may be 1,35 bps INFO @ Fri, 26 Jun 2020 22:39:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494822/SRX494822.10_model.r WARNING @ Fri, 26 Jun 2020 22:39:09: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:39:09: #2 You may need to consider one of the other alternative d(s): 1,35 WARNING @ Fri, 26 Jun 2020 22:39:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:39:09: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:39:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:39:17: 12000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:39:27: 13000000 INFO @ Fri, 26 Jun 2020 22:39:34: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:39:37: 14000000 INFO @ Fri, 26 Jun 2020 22:39:38: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 22:39:38: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 22:39:38: #1 total tags in treatment: 14052804 INFO @ Fri, 26 Jun 2020 22:39:38: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:39:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:39:38: #1 tags after filtering in treatment: 14052804 INFO @ Fri, 26 Jun 2020 22:39:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:39:38: #1 finished! INFO @ Fri, 26 Jun 2020 22:39:38: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:39:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:39:39: #2 number of paired peaks: 257 WARNING @ Fri, 26 Jun 2020 22:39:39: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Fri, 26 Jun 2020 22:39:39: start model_add_line... INFO @ Fri, 26 Jun 2020 22:39:39: start X-correlation... INFO @ Fri, 26 Jun 2020 22:39:39: end of X-cor INFO @ Fri, 26 Jun 2020 22:39:39: #2 finished! INFO @ Fri, 26 Jun 2020 22:39:39: #2 predicted fragment length is 35 bps INFO @ Fri, 26 Jun 2020 22:39:39: #2 alternative fragment length(s) may be 1,35 bps INFO @ Fri, 26 Jun 2020 22:39:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494822/SRX494822.20_model.r WARNING @ Fri, 26 Jun 2020 22:39:39: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:39:39: #2 You may need to consider one of the other alternative d(s): 1,35 WARNING @ Fri, 26 Jun 2020 22:39:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:39:39: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:39:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:39:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494822/SRX494822.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:39:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494822/SRX494822.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:39:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494822/SRX494822.10_summits.bed INFO @ Fri, 26 Jun 2020 22:39:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (577 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:40:04: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:40:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494822/SRX494822.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:40:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494822/SRX494822.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:40:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494822/SRX494822.20_summits.bed INFO @ Fri, 26 Jun 2020 22:40:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (123 records, 4 fields): 3 millis CompletedMACS2peakCalling