Job ID = 14160715 SRX = SRX10569203 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2021-12-08T18:52:13 prefetch.2.10.7: 1) Downloading 'SRR14202289'... 2021-12-08T18:52:13 prefetch.2.10.7: Downloading via HTTPS... 2021-12-08T18:57:35 prefetch.2.10.7: HTTPS download succeed 2021-12-08T18:57:35 prefetch.2.10.7: 1) 'SRR14202289' was downloaded successfully 2021-12-08T18:57:35 prefetch.2.10.7: 'SRR14202289' has 0 unresolved dependencies Read 28979654 spots for SRR14202289/SRR14202289.sra Written 28979654 spots for SRR14202289/SRR14202289.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160877 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:05 28979654 reads; of these: 28979654 (100.00%) were unpaired; of these: 9178007 (31.67%) aligned 0 times 15859487 (54.73%) aligned exactly 1 time 3942160 (13.60%) aligned >1 times 68.33% overall alignment rate Time searching: 00:10:05 Overall time: 00:10:05 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_sort_core] merging from 12 files... [bam_rmdupse_core] 2968852 / 19801647 = 0.1499 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 04:15:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10569203/SRX10569203.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10569203/SRX10569203.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10569203/SRX10569203.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10569203/SRX10569203.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 @ Thu, 09 Dec 2021 04:15:22: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:15:22: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:15:27: 1000000 INFO @ Thu, 09 Dec 2021 04:15:33: 2000000 INFO @ Thu, 09 Dec 2021 04:15:39: 3000000 INFO @ Thu, 09 Dec 2021 04:15:44: 4000000 INFO @ Thu, 09 Dec 2021 04:15:50: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 04:15:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10569203/SRX10569203.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10569203/SRX10569203.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10569203/SRX10569203.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10569203/SRX10569203.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 @ Thu, 09 Dec 2021 04:15:52: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:15:52: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:15:56: 6000000 INFO @ Thu, 09 Dec 2021 04:15:59: 1000000 INFO @ Thu, 09 Dec 2021 04:16:02: 7000000 INFO @ Thu, 09 Dec 2021 04:16:07: 2000000 INFO @ Thu, 09 Dec 2021 04:16:09: 8000000 INFO @ Thu, 09 Dec 2021 04:16:15: 3000000 INFO @ Thu, 09 Dec 2021 04:16:15: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 04:16:21: 10000000 INFO @ Thu, 09 Dec 2021 04:16:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10569203/SRX10569203.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10569203/SRX10569203.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10569203/SRX10569203.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10569203/SRX10569203.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 @ Thu, 09 Dec 2021 04:16:22: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:16:22: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:16:22: 4000000 INFO @ Thu, 09 Dec 2021 04:16:28: 11000000 INFO @ Thu, 09 Dec 2021 04:16:29: 5000000 INFO @ Thu, 09 Dec 2021 04:16:29: 1000000 INFO @ Thu, 09 Dec 2021 04:16:34: 12000000 INFO @ Thu, 09 Dec 2021 04:16:37: 6000000 INFO @ Thu, 09 Dec 2021 04:16:37: 2000000 INFO @ Thu, 09 Dec 2021 04:16:40: 13000000 INFO @ Thu, 09 Dec 2021 04:16:44: 7000000 INFO @ Thu, 09 Dec 2021 04:16:44: 3000000 INFO @ Thu, 09 Dec 2021 04:16:47: 14000000 INFO @ Thu, 09 Dec 2021 04:16:51: 8000000 INFO @ Thu, 09 Dec 2021 04:16:52: 4000000 INFO @ Thu, 09 Dec 2021 04:16:53: 15000000 INFO @ Thu, 09 Dec 2021 04:16:59: 9000000 INFO @ Thu, 09 Dec 2021 04:16:59: 5000000 INFO @ Thu, 09 Dec 2021 04:17:00: 16000000 INFO @ Thu, 09 Dec 2021 04:17:05: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 04:17:05: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 04:17:05: #1 total tags in treatment: 16832795 INFO @ Thu, 09 Dec 2021 04:17:05: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:17:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:17:05: #1 tags after filtering in treatment: 16832795 INFO @ Thu, 09 Dec 2021 04:17:05: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:17:05: #1 finished! INFO @ Thu, 09 Dec 2021 04:17:05: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:17:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:17:06: 6000000 INFO @ Thu, 09 Dec 2021 04:17:06: 10000000 INFO @ Thu, 09 Dec 2021 04:17:06: #2 number of paired peaks: 252 WARNING @ Thu, 09 Dec 2021 04:17:06: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Thu, 09 Dec 2021 04:17:06: start model_add_line... INFO @ Thu, 09 Dec 2021 04:17:06: start X-correlation... INFO @ Thu, 09 Dec 2021 04:17:06: end of X-cor INFO @ Thu, 09 Dec 2021 04:17:06: #2 finished! INFO @ Thu, 09 Dec 2021 04:17:06: #2 predicted fragment length is 46 bps INFO @ Thu, 09 Dec 2021 04:17:06: #2 alternative fragment length(s) may be 2,46,522 bps INFO @ Thu, 09 Dec 2021 04:17:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10569203/SRX10569203.05_model.r WARNING @ Thu, 09 Dec 2021 04:17:06: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:17:06: #2 You may need to consider one of the other alternative d(s): 2,46,522 WARNING @ Thu, 09 Dec 2021 04:17:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:17:06: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:17:06: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:17:13: 7000000 INFO @ Thu, 09 Dec 2021 04:17:13: 11000000 INFO @ Thu, 09 Dec 2021 04:17:20: 8000000 INFO @ Thu, 09 Dec 2021 04:17:21: 12000000 INFO @ Thu, 09 Dec 2021 04:17:27: 9000000 INFO @ Thu, 09 Dec 2021 04:17:28: 13000000 INFO @ Thu, 09 Dec 2021 04:17:33: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:17:35: 10000000 INFO @ Thu, 09 Dec 2021 04:17:36: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 04:17:42: 11000000 INFO @ Thu, 09 Dec 2021 04:17:43: 15000000 INFO @ Thu, 09 Dec 2021 04:17:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10569203/SRX10569203.05_peaks.xls INFO @ Thu, 09 Dec 2021 04:17:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10569203/SRX10569203.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:17:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10569203/SRX10569203.05_summits.bed INFO @ Thu, 09 Dec 2021 04:17:46: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (667 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:17:49: 12000000 INFO @ Thu, 09 Dec 2021 04:17:50: 16000000 INFO @ Thu, 09 Dec 2021 04:17:56: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 04:17:56: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 04:17:56: #1 total tags in treatment: 16832795 INFO @ Thu, 09 Dec 2021 04:17:56: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:17:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:17:56: #1 tags after filtering in treatment: 16832795 INFO @ Thu, 09 Dec 2021 04:17:56: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:17:56: #1 finished! INFO @ Thu, 09 Dec 2021 04:17:56: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:17:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:17:57: 13000000 INFO @ Thu, 09 Dec 2021 04:17:57: #2 number of paired peaks: 252 WARNING @ Thu, 09 Dec 2021 04:17:57: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Thu, 09 Dec 2021 04:17:57: start model_add_line... INFO @ Thu, 09 Dec 2021 04:17:57: start X-correlation... INFO @ Thu, 09 Dec 2021 04:17:57: end of X-cor INFO @ Thu, 09 Dec 2021 04:17:57: #2 finished! INFO @ Thu, 09 Dec 2021 04:17:57: #2 predicted fragment length is 46 bps INFO @ Thu, 09 Dec 2021 04:17:57: #2 alternative fragment length(s) may be 2,46,522 bps INFO @ Thu, 09 Dec 2021 04:17:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10569203/SRX10569203.10_model.r WARNING @ Thu, 09 Dec 2021 04:17:57: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:17:57: #2 You may need to consider one of the other alternative d(s): 2,46,522 WARNING @ Thu, 09 Dec 2021 04:17:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:17:57: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:17:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:18:04: 14000000 INFO @ Thu, 09 Dec 2021 04:18:11: 15000000 INFO @ Thu, 09 Dec 2021 04:18:17: 16000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 04:18:23: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 04:18:23: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 04:18:23: #1 total tags in treatment: 16832795 INFO @ Thu, 09 Dec 2021 04:18:23: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:18:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:18:23: #1 tags after filtering in treatment: 16832795 INFO @ Thu, 09 Dec 2021 04:18:23: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:18:23: #1 finished! INFO @ Thu, 09 Dec 2021 04:18:23: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:18:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:18:24: #2 number of paired peaks: 252 WARNING @ Thu, 09 Dec 2021 04:18:24: Fewer paired peaks (252) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 252 pairs to build model! INFO @ Thu, 09 Dec 2021 04:18:24: start model_add_line... INFO @ Thu, 09 Dec 2021 04:18:24: start X-correlation... INFO @ Thu, 09 Dec 2021 04:18:24: end of X-cor INFO @ Thu, 09 Dec 2021 04:18:24: #2 finished! INFO @ Thu, 09 Dec 2021 04:18:24: #2 predicted fragment length is 46 bps INFO @ Thu, 09 Dec 2021 04:18:24: #2 alternative fragment length(s) may be 2,46,522 bps INFO @ Thu, 09 Dec 2021 04:18:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10569203/SRX10569203.20_model.r WARNING @ Thu, 09 Dec 2021 04:18:24: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:18:24: #2 You may need to consider one of the other alternative d(s): 2,46,522 WARNING @ Thu, 09 Dec 2021 04:18:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:18:24: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:18:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:18:25: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:18:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10569203/SRX10569203.10_peaks.xls INFO @ Thu, 09 Dec 2021 04:18:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10569203/SRX10569203.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:18:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10569203/SRX10569203.10_summits.bed INFO @ Thu, 09 Dec 2021 04:18:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (426 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:18:53: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:19:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10569203/SRX10569203.20_peaks.xls INFO @ Thu, 09 Dec 2021 04:19:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10569203/SRX10569203.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:19:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10569203/SRX10569203.20_summits.bed INFO @ Thu, 09 Dec 2021 04:19:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (159 records, 4 fields): 1 millis CompletedMACS2peakCalling