Job ID = 10165683 SRX = SRX8331159 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 38052982 spots for SRR11778472/SRR11778472.sra Written 38052982 spots for SRR11778472/SRR11778472.sra fastq に変換しました。 bowtie でマッピング中... Your job 10166038 ("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: 00:15:39 38052982 reads; of these: 38052982 (100.00%) were unpaired; of these: 163292 (0.43%) aligned 0 times 32328540 (84.96%) aligned exactly 1 time 5561150 (14.61%) aligned >1 times 99.57% overall alignment rate Time searching: 00:15:39 Overall time: 00:15:39 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 16 files... [bam_rmdupse_core] 24440650 / 37889690 = 0.6450 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 @ Thu, 08 Oct 2020 20:00:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.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, 08 Oct 2020 20:00:49: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:00:49: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:00:57: 1000000 INFO @ Thu, 08 Oct 2020 20:01:05: 2000000 INFO @ Thu, 08 Oct 2020 20:01:13: 3000000 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 @ Thu, 08 Oct 2020 20:01:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.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, 08 Oct 2020 20:01:18: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:01:18: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:01:21: 4000000 INFO @ Thu, 08 Oct 2020 20:01:26: 1000000 INFO @ Thu, 08 Oct 2020 20:01:29: 5000000 INFO @ Thu, 08 Oct 2020 20:01:33: 2000000 INFO @ Thu, 08 Oct 2020 20:01:37: 6000000 INFO @ Thu, 08 Oct 2020 20:01:41: 3000000 INFO @ Thu, 08 Oct 2020 20:01:44: 7000000 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 @ Thu, 08 Oct 2020 20:01:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.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, 08 Oct 2020 20:01:48: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:01:48: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:01:49: 4000000 INFO @ Thu, 08 Oct 2020 20:01:52: 8000000 INFO @ Thu, 08 Oct 2020 20:01:57: 5000000 INFO @ Thu, 08 Oct 2020 20:01:57: 1000000 INFO @ Thu, 08 Oct 2020 20:02:00: 9000000 INFO @ Thu, 08 Oct 2020 20:02:04: 6000000 INFO @ Thu, 08 Oct 2020 20:02:07: 2000000 INFO @ Thu, 08 Oct 2020 20:02:08: 10000000 INFO @ Thu, 08 Oct 2020 20:02:12: 7000000 INFO @ Thu, 08 Oct 2020 20:02:16: 11000000 INFO @ Thu, 08 Oct 2020 20:02:16: 3000000 INFO @ Thu, 08 Oct 2020 20:02:20: 8000000 INFO @ Thu, 08 Oct 2020 20:02:23: 12000000 INFO @ Thu, 08 Oct 2020 20:02:25: 4000000 INFO @ Thu, 08 Oct 2020 20:02:28: 9000000 INFO @ Thu, 08 Oct 2020 20:02:31: 13000000 INFO @ Thu, 08 Oct 2020 20:02:34: 5000000 INFO @ Thu, 08 Oct 2020 20:02:35: #1 tag size is determined as 51 bps INFO @ Thu, 08 Oct 2020 20:02:35: #1 tag size = 51 INFO @ Thu, 08 Oct 2020 20:02:35: #1 total tags in treatment: 13449040 INFO @ Thu, 08 Oct 2020 20:02:35: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:02:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:02:35: #1 tags after filtering in treatment: 13449040 INFO @ Thu, 08 Oct 2020 20:02:35: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:02:35: #1 finished! INFO @ Thu, 08 Oct 2020 20:02:35: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:02:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:02:36: #2 number of paired peaks: 420 WARNING @ Thu, 08 Oct 2020 20:02:36: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Thu, 08 Oct 2020 20:02:36: start model_add_line... INFO @ Thu, 08 Oct 2020 20:02:36: 10000000 INFO @ Thu, 08 Oct 2020 20:02:36: start X-correlation... INFO @ Thu, 08 Oct 2020 20:02:36: end of X-cor INFO @ Thu, 08 Oct 2020 20:02:36: #2 finished! INFO @ Thu, 08 Oct 2020 20:02:36: #2 predicted fragment length is 68 bps INFO @ Thu, 08 Oct 2020 20:02:36: #2 alternative fragment length(s) may be 3,68 bps INFO @ Thu, 08 Oct 2020 20:02:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.05_model.r WARNING @ Thu, 08 Oct 2020 20:02:36: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:02:36: #2 You may need to consider one of the other alternative d(s): 3,68 WARNING @ Thu, 08 Oct 2020 20:02:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:02:36: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:02:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:02:44: 6000000 INFO @ Thu, 08 Oct 2020 20:02:44: 11000000 INFO @ Thu, 08 Oct 2020 20:02:52: 12000000 INFO @ Thu, 08 Oct 2020 20:02:53: 7000000 INFO @ Thu, 08 Oct 2020 20:03:00: 13000000 INFO @ Thu, 08 Oct 2020 20:03:02: 8000000 INFO @ Thu, 08 Oct 2020 20:03:02: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:03:04: #1 tag size is determined as 51 bps INFO @ Thu, 08 Oct 2020 20:03:04: #1 tag size = 51 INFO @ Thu, 08 Oct 2020 20:03:04: #1 total tags in treatment: 13449040 INFO @ Thu, 08 Oct 2020 20:03:04: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:03:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:03:04: #1 tags after filtering in treatment: 13449040 INFO @ Thu, 08 Oct 2020 20:03:04: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:03:04: #1 finished! INFO @ Thu, 08 Oct 2020 20:03:04: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:03:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:03:05: #2 number of paired peaks: 420 WARNING @ Thu, 08 Oct 2020 20:03:05: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Thu, 08 Oct 2020 20:03:05: start model_add_line... INFO @ Thu, 08 Oct 2020 20:03:05: start X-correlation... INFO @ Thu, 08 Oct 2020 20:03:05: end of X-cor INFO @ Thu, 08 Oct 2020 20:03:05: #2 finished! INFO @ Thu, 08 Oct 2020 20:03:05: #2 predicted fragment length is 68 bps INFO @ Thu, 08 Oct 2020 20:03:05: #2 alternative fragment length(s) may be 3,68 bps INFO @ Thu, 08 Oct 2020 20:03:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.10_model.r WARNING @ Thu, 08 Oct 2020 20:03:05: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:03:05: #2 You may need to consider one of the other alternative d(s): 3,68 WARNING @ Thu, 08 Oct 2020 20:03:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:03:05: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:03:05: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:03:11: 9000000 INFO @ Thu, 08 Oct 2020 20:03:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:03:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:03:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.05_summits.bed INFO @ Thu, 08 Oct 2020 20:03:18: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (13880 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:03:20: 10000000 INFO @ Thu, 08 Oct 2020 20:03:29: 11000000 INFO @ Thu, 08 Oct 2020 20:03:31: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:03:39: 12000000 INFO @ Thu, 08 Oct 2020 20:03:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:03:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:03:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.10_summits.bed INFO @ Thu, 08 Oct 2020 20:03:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2291 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:03:48: 13000000 BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:03:52: #1 tag size is determined as 51 bps INFO @ Thu, 08 Oct 2020 20:03:52: #1 tag size = 51 INFO @ Thu, 08 Oct 2020 20:03:52: #1 total tags in treatment: 13449040 INFO @ Thu, 08 Oct 2020 20:03:52: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:03:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:03:52: #1 tags after filtering in treatment: 13449040 INFO @ Thu, 08 Oct 2020 20:03:52: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:03:52: #1 finished! INFO @ Thu, 08 Oct 2020 20:03:52: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:03:52: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:03:53: #2 number of paired peaks: 420 WARNING @ Thu, 08 Oct 2020 20:03:53: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Thu, 08 Oct 2020 20:03:53: start model_add_line... INFO @ Thu, 08 Oct 2020 20:03:53: start X-correlation... INFO @ Thu, 08 Oct 2020 20:03:53: end of X-cor INFO @ Thu, 08 Oct 2020 20:03:53: #2 finished! INFO @ Thu, 08 Oct 2020 20:03:53: #2 predicted fragment length is 68 bps INFO @ Thu, 08 Oct 2020 20:03:53: #2 alternative fragment length(s) may be 3,68 bps INFO @ Thu, 08 Oct 2020 20:03:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.20_model.r WARNING @ Thu, 08 Oct 2020 20:03:53: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:03:53: #2 You may need to consider one of the other alternative d(s): 3,68 WARNING @ Thu, 08 Oct 2020 20:03:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:03:53: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:03:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:04:19: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:04:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:04:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:04:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.20_summits.bed INFO @ Thu, 08 Oct 2020 20:04:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (432 records, 4 fields): 2 millis CompletedMACS2peakCalling