Job ID = 6367046 SRX = SRX2761391 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:15:31 prefetch.2.10.7: 1) Downloading 'SRR5476965'... 2020-06-15T23:15:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:17:15 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:17:15 prefetch.2.10.7: 1) 'SRR5476965' was downloaded successfully Read 15267767 spots for SRR5476965/SRR5476965.sra Written 15267767 spots for SRR5476965/SRR5476965.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: 00:03:28 15267767 reads; of these: 15267767 (100.00%) were unpaired; of these: 1024451 (6.71%) aligned 0 times 11693842 (76.59%) aligned exactly 1 time 2549474 (16.70%) aligned >1 times 93.29% overall alignment rate Time searching: 00:03:28 Overall time: 00:03:28 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] 1098440 / 14243316 = 0.0771 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 08:25:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2761391/SRX2761391.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2761391/SRX2761391.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2761391/SRX2761391.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2761391/SRX2761391.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 08:25:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:27: 1000000 INFO @ Tue, 16 Jun 2020 08:25:33: 2000000 INFO @ Tue, 16 Jun 2020 08:25:39: 3000000 INFO @ Tue, 16 Jun 2020 08:25:44: 4000000 INFO @ Tue, 16 Jun 2020 08:25:50: 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 08:25:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2761391/SRX2761391.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2761391/SRX2761391.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2761391/SRX2761391.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2761391/SRX2761391.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 08:25:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:56: 6000000 INFO @ Tue, 16 Jun 2020 08:25:58: 1000000 INFO @ Tue, 16 Jun 2020 08:26:02: 7000000 INFO @ Tue, 16 Jun 2020 08:26:04: 2000000 INFO @ Tue, 16 Jun 2020 08:26:08: 8000000 INFO @ Tue, 16 Jun 2020 08:26:10: 3000000 INFO @ Tue, 16 Jun 2020 08:26:14: 9000000 INFO @ Tue, 16 Jun 2020 08:26:16: 4000000 INFO @ Tue, 16 Jun 2020 08:26:19: 10000000 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 08:26:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2761391/SRX2761391.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2761391/SRX2761391.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2761391/SRX2761391.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2761391/SRX2761391.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 08:26:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:26:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:26:22: 5000000 INFO @ Tue, 16 Jun 2020 08:26:26: 11000000 INFO @ Tue, 16 Jun 2020 08:26:28: 1000000 INFO @ Tue, 16 Jun 2020 08:26:28: 6000000 INFO @ Tue, 16 Jun 2020 08:26:32: 12000000 INFO @ Tue, 16 Jun 2020 08:26:35: 7000000 INFO @ Tue, 16 Jun 2020 08:26:35: 2000000 INFO @ Tue, 16 Jun 2020 08:26:38: 13000000 INFO @ Tue, 16 Jun 2020 08:26:39: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:26:39: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:26:39: #1 total tags in treatment: 13144876 INFO @ Tue, 16 Jun 2020 08:26:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:26:39: #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 08:26:40: #1 tags after filtering in treatment: 13144876 INFO @ Tue, 16 Jun 2020 08:26:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:26:40: #1 finished! INFO @ Tue, 16 Jun 2020 08:26:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:26:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:26:40: #2 number of paired peaks: 355 WARNING @ Tue, 16 Jun 2020 08:26:40: Fewer paired peaks (355) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 355 pairs to build model! INFO @ Tue, 16 Jun 2020 08:26:40: start model_add_line... INFO @ Tue, 16 Jun 2020 08:26:41: start X-correlation... INFO @ Tue, 16 Jun 2020 08:26:41: end of X-cor INFO @ Tue, 16 Jun 2020 08:26:41: #2 finished! INFO @ Tue, 16 Jun 2020 08:26:41: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 08:26:41: #2 alternative fragment length(s) may be 2,44 bps INFO @ Tue, 16 Jun 2020 08:26:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2761391/SRX2761391.05_model.r WARNING @ Tue, 16 Jun 2020 08:26:41: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:26:41: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Tue, 16 Jun 2020 08:26:41: #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 08:26:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:26:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:26:41: 8000000 INFO @ Tue, 16 Jun 2020 08:26:41: 3000000 INFO @ Tue, 16 Jun 2020 08:26:48: 9000000 INFO @ Tue, 16 Jun 2020 08:26:48: 4000000 INFO @ Tue, 16 Jun 2020 08:26:54: 10000000 INFO @ Tue, 16 Jun 2020 08:26:54: 5000000 INFO @ Tue, 16 Jun 2020 08:27:00: 11000000 INFO @ Tue, 16 Jun 2020 08:27:01: 6000000 INFO @ Tue, 16 Jun 2020 08:27:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:27:06: 12000000 INFO @ Tue, 16 Jun 2020 08:27:07: 7000000 INFO @ Tue, 16 Jun 2020 08:27:13: 13000000 INFO @ Tue, 16 Jun 2020 08:27:13: 8000000 INFO @ Tue, 16 Jun 2020 08:27:14: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:27:14: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:27:14: #1 total tags in treatment: 13144876 INFO @ Tue, 16 Jun 2020 08:27:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:27:14: #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 08:27:14: #1 tags after filtering in treatment: 13144876 INFO @ Tue, 16 Jun 2020 08:27:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:27:14: #1 finished! INFO @ Tue, 16 Jun 2020 08:27:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:27:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:27:15: #2 number of paired peaks: 355 WARNING @ Tue, 16 Jun 2020 08:27:15: Fewer paired peaks (355) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 355 pairs to build model! INFO @ Tue, 16 Jun 2020 08:27:15: start model_add_line... INFO @ Tue, 16 Jun 2020 08:27:15: start X-correlation... INFO @ Tue, 16 Jun 2020 08:27:15: end of X-cor INFO @ Tue, 16 Jun 2020 08:27:15: #2 finished! INFO @ Tue, 16 Jun 2020 08:27:15: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 08:27:15: #2 alternative fragment length(s) may be 2,44 bps INFO @ Tue, 16 Jun 2020 08:27:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2761391/SRX2761391.10_model.r WARNING @ Tue, 16 Jun 2020 08:27:15: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:27:15: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Tue, 16 Jun 2020 08:27:15: #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 08:27:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:27:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:27:19: 9000000 INFO @ Tue, 16 Jun 2020 08:27:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2761391/SRX2761391.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:27:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2761391/SRX2761391.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:27:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2761391/SRX2761391.05_summits.bed INFO @ Tue, 16 Jun 2020 08:27:19: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (706 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:27:25: 10000000 INFO @ Tue, 16 Jun 2020 08:27:31: 11000000 INFO @ Tue, 16 Jun 2020 08:27:37: 12000000 INFO @ Tue, 16 Jun 2020 08:27:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:27:43: 13000000 INFO @ Tue, 16 Jun 2020 08:27:44: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:27:44: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:27:44: #1 total tags in treatment: 13144876 INFO @ Tue, 16 Jun 2020 08:27:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:27:44: #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 08:27:44: #1 tags after filtering in treatment: 13144876 INFO @ Tue, 16 Jun 2020 08:27:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:27:44: #1 finished! INFO @ Tue, 16 Jun 2020 08:27:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:27:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:27:45: #2 number of paired peaks: 355 WARNING @ Tue, 16 Jun 2020 08:27:45: Fewer paired peaks (355) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 355 pairs to build model! INFO @ Tue, 16 Jun 2020 08:27:45: start model_add_line... INFO @ Tue, 16 Jun 2020 08:27:45: start X-correlation... INFO @ Tue, 16 Jun 2020 08:27:45: end of X-cor INFO @ Tue, 16 Jun 2020 08:27:45: #2 finished! INFO @ Tue, 16 Jun 2020 08:27:45: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 08:27:45: #2 alternative fragment length(s) may be 2,44 bps INFO @ Tue, 16 Jun 2020 08:27:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2761391/SRX2761391.20_model.r WARNING @ Tue, 16 Jun 2020 08:27:45: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:27:45: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Tue, 16 Jun 2020 08:27:45: #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 08:27:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:27:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:27:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2761391/SRX2761391.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:27:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2761391/SRX2761391.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:27:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2761391/SRX2761391.10_summits.bed INFO @ Tue, 16 Jun 2020 08:27:53: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (474 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:28:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:28:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2761391/SRX2761391.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:28:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2761391/SRX2761391.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:28:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2761391/SRX2761391.20_summits.bed INFO @ Tue, 16 Jun 2020 08:28:23: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (180 records, 4 fields): 2 millis CompletedMACS2peakCalling