Job ID = 6626419 SRX = SRX7262242 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 2274836 spots for SRR10581865/SRR10581865.sra Written 2274836 spots for SRR10581865/SRR10581865.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626512 ("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: 00:00:26 2274836 reads; of these: 2274836 (100.00%) were unpaired; of these: 967136 (42.51%) aligned 0 times 994802 (43.73%) aligned exactly 1 time 312898 (13.75%) aligned >1 times 57.49% overall alignment rate Time searching: 00:00:26 Overall time: 00:00:26 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] 82315 / 1307700 = 0.0629 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, 14 Jul 2020 07:01:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262242/SRX7262242.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262242/SRX7262242.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262242/SRX7262242.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262242/SRX7262242.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, 14 Jul 2020 07:01:30: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:01:30: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:01:38: 1000000 INFO @ Tue, 14 Jul 2020 07:01:39: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:01:39: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:01:39: #1 total tags in treatment: 1225385 INFO @ Tue, 14 Jul 2020 07:01:39: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:01:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:01:39: #1 tags after filtering in treatment: 1225385 INFO @ Tue, 14 Jul 2020 07:01:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:01:39: #1 finished! INFO @ Tue, 14 Jul 2020 07:01:39: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:01:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:01:39: #2 number of paired peaks: 735 WARNING @ Tue, 14 Jul 2020 07:01:39: Fewer paired peaks (735) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 735 pairs to build model! INFO @ Tue, 14 Jul 2020 07:01:39: start model_add_line... INFO @ Tue, 14 Jul 2020 07:01:39: start X-correlation... INFO @ Tue, 14 Jul 2020 07:01:39: end of X-cor INFO @ Tue, 14 Jul 2020 07:01:39: #2 finished! INFO @ Tue, 14 Jul 2020 07:01:39: #2 predicted fragment length is 51 bps INFO @ Tue, 14 Jul 2020 07:01:39: #2 alternative fragment length(s) may be 51,152,377,495,521 bps INFO @ Tue, 14 Jul 2020 07:01:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262242/SRX7262242.05_model.r WARNING @ Tue, 14 Jul 2020 07:01:39: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:01:39: #2 You may need to consider one of the other alternative d(s): 51,152,377,495,521 WARNING @ Tue, 14 Jul 2020 07:01:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:01:39: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:01:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:01:42: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:01:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262242/SRX7262242.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:01:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262242/SRX7262242.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:01:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262242/SRX7262242.05_summits.bed INFO @ Tue, 14 Jul 2020 07:01:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (340 records, 4 fields): 18 millis CompletedMACS2peakCalling 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, 14 Jul 2020 07:02:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262242/SRX7262242.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262242/SRX7262242.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262242/SRX7262242.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262242/SRX7262242.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, 14 Jul 2020 07:02:00: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:02:00: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:02:06: 1000000 INFO @ Tue, 14 Jul 2020 07:02:07: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:02:07: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:02:07: #1 total tags in treatment: 1225385 INFO @ Tue, 14 Jul 2020 07:02:07: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:02:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:02:07: #1 tags after filtering in treatment: 1225385 INFO @ Tue, 14 Jul 2020 07:02:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:02:07: #1 finished! INFO @ Tue, 14 Jul 2020 07:02:07: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:02:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:02:07: #2 number of paired peaks: 735 WARNING @ Tue, 14 Jul 2020 07:02:07: Fewer paired peaks (735) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 735 pairs to build model! INFO @ Tue, 14 Jul 2020 07:02:07: start model_add_line... INFO @ Tue, 14 Jul 2020 07:02:07: start X-correlation... INFO @ Tue, 14 Jul 2020 07:02:07: end of X-cor INFO @ Tue, 14 Jul 2020 07:02:07: #2 finished! INFO @ Tue, 14 Jul 2020 07:02:07: #2 predicted fragment length is 51 bps INFO @ Tue, 14 Jul 2020 07:02:07: #2 alternative fragment length(s) may be 51,152,377,495,521 bps INFO @ Tue, 14 Jul 2020 07:02:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262242/SRX7262242.10_model.r WARNING @ Tue, 14 Jul 2020 07:02:07: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:02:07: #2 You may need to consider one of the other alternative d(s): 51,152,377,495,521 WARNING @ Tue, 14 Jul 2020 07:02:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:02:07: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:02:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:02:10: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:02:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262242/SRX7262242.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:02:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262242/SRX7262242.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:02:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262242/SRX7262242.10_summits.bed INFO @ Tue, 14 Jul 2020 07:02:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (191 records, 4 fields): 1 millis CompletedMACS2peakCalling 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, 14 Jul 2020 07:02:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7262242/SRX7262242.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7262242/SRX7262242.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7262242/SRX7262242.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7262242/SRX7262242.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, 14 Jul 2020 07:02:31: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:02:31: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:02:39: 1000000 INFO @ Tue, 14 Jul 2020 07:02:40: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 07:02:40: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 07:02:40: #1 total tags in treatment: 1225385 INFO @ Tue, 14 Jul 2020 07:02:40: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:02:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:02:40: #1 tags after filtering in treatment: 1225385 INFO @ Tue, 14 Jul 2020 07:02:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 07:02:40: #1 finished! INFO @ Tue, 14 Jul 2020 07:02:40: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:02:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:02:41: #2 number of paired peaks: 735 WARNING @ Tue, 14 Jul 2020 07:02:41: Fewer paired peaks (735) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 735 pairs to build model! INFO @ Tue, 14 Jul 2020 07:02:41: start model_add_line... INFO @ Tue, 14 Jul 2020 07:02:41: start X-correlation... INFO @ Tue, 14 Jul 2020 07:02:41: end of X-cor INFO @ Tue, 14 Jul 2020 07:02:41: #2 finished! INFO @ Tue, 14 Jul 2020 07:02:41: #2 predicted fragment length is 51 bps INFO @ Tue, 14 Jul 2020 07:02:41: #2 alternative fragment length(s) may be 51,152,377,495,521 bps INFO @ Tue, 14 Jul 2020 07:02:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7262242/SRX7262242.20_model.r WARNING @ Tue, 14 Jul 2020 07:02:41: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 07:02:41: #2 You may need to consider one of the other alternative d(s): 51,152,377,495,521 WARNING @ Tue, 14 Jul 2020 07:02:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 07:02:41: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:02:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:02:44: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:02:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7262242/SRX7262242.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:02:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7262242/SRX7262242.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:02:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7262242/SRX7262242.20_summits.bed INFO @ Tue, 14 Jul 2020 07:02:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (78 records, 4 fields): 16 millis CompletedMACS2peakCalling