Job ID = 16434969 SRX = SRX10435537 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 9949032 spots for SRR14060937/SRR14060937.sra Written 9949032 spots for SRR14060937/SRR14060937.sra fastq に変換しました。 bowtie でマッピング中... Your job 16435013 ("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: 00:04:03 9949032 reads; of these: 9949032 (100.00%) were unpaired; of these: 826922 (8.31%) aligned 0 times 7627764 (76.67%) aligned exactly 1 time 1494346 (15.02%) aligned >1 times 91.69% overall alignment rate Time searching: 00:04:03 Overall time: 00:04:03 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] 915080 / 9122110 = 0.1003 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:29:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435537/SRX10435537.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435537/SRX10435537.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435537/SRX10435537.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435537/SRX10435537.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, 02 Aug 2022 10:29:46: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:29:46: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:29:53: 1000000 INFO @ Tue, 02 Aug 2022 10:30:00: 2000000 INFO @ Tue, 02 Aug 2022 10:30:07: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:30:14: 4000000 INFO @ Tue, 02 Aug 2022 10:30:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435537/SRX10435537.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435537/SRX10435537.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435537/SRX10435537.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435537/SRX10435537.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, 02 Aug 2022 10:30:16: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:30:16: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:30:23: 5000000 INFO @ Tue, 02 Aug 2022 10:30:24: 1000000 INFO @ Tue, 02 Aug 2022 10:30:31: 6000000 INFO @ Tue, 02 Aug 2022 10:30:32: 2000000 INFO @ Tue, 02 Aug 2022 10:30:39: 7000000 INFO @ Tue, 02 Aug 2022 10:30:41: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:30:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435537/SRX10435537.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435537/SRX10435537.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435537/SRX10435537.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435537/SRX10435537.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, 02 Aug 2022 10:30:47: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:30:47: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:30:47: 8000000 INFO @ Tue, 02 Aug 2022 10:30:49: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:30:49: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:30:49: #1 total tags in treatment: 8207030 INFO @ Tue, 02 Aug 2022 10:30:49: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:30:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:30:49: #1 tags after filtering in treatment: 8207030 INFO @ Tue, 02 Aug 2022 10:30:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:30:49: #1 finished! INFO @ Tue, 02 Aug 2022 10:30:49: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:30:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:30:49: 4000000 INFO @ Tue, 02 Aug 2022 10:30:50: #2 number of paired peaks: 694 WARNING @ Tue, 02 Aug 2022 10:30:50: Fewer paired peaks (694) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 694 pairs to build model! INFO @ Tue, 02 Aug 2022 10:30:50: start model_add_line... INFO @ Tue, 02 Aug 2022 10:30:50: start X-correlation... INFO @ Tue, 02 Aug 2022 10:30:50: end of X-cor INFO @ Tue, 02 Aug 2022 10:30:50: #2 finished! INFO @ Tue, 02 Aug 2022 10:30:50: #2 predicted fragment length is 144 bps INFO @ Tue, 02 Aug 2022 10:30:50: #2 alternative fragment length(s) may be 144 bps INFO @ Tue, 02 Aug 2022 10:30:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435537/SRX10435537.05_model.r WARNING @ Tue, 02 Aug 2022 10:30:50: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:30:50: #2 You may need to consider one of the other alternative d(s): 144 WARNING @ Tue, 02 Aug 2022 10:30:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:30:50: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:30:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:30:55: 1000000 INFO @ Tue, 02 Aug 2022 10:30:57: 5000000 INFO @ Tue, 02 Aug 2022 10:31:03: 2000000 INFO @ Tue, 02 Aug 2022 10:31:05: 6000000 INFO @ Tue, 02 Aug 2022 10:31:10: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:31:12: 7000000 INFO @ Tue, 02 Aug 2022 10:31:15: 3000000 INFO @ Tue, 02 Aug 2022 10:31:19: 8000000 INFO @ Tue, 02 Aug 2022 10:31:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435537/SRX10435537.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:31:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435537/SRX10435537.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:31:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435537/SRX10435537.05_summits.bed INFO @ Tue, 02 Aug 2022 10:31:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2325 records, 4 fields): 51 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:31:21: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:31:21: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:31:21: #1 total tags in treatment: 8207030 INFO @ Tue, 02 Aug 2022 10:31:21: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:31:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:31:21: #1 tags after filtering in treatment: 8207030 INFO @ Tue, 02 Aug 2022 10:31:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:31:21: #1 finished! INFO @ Tue, 02 Aug 2022 10:31:21: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:31:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:31:22: #2 number of paired peaks: 694 WARNING @ Tue, 02 Aug 2022 10:31:22: Fewer paired peaks (694) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 694 pairs to build model! INFO @ Tue, 02 Aug 2022 10:31:22: start model_add_line... INFO @ Tue, 02 Aug 2022 10:31:22: start X-correlation... INFO @ Tue, 02 Aug 2022 10:31:22: end of X-cor INFO @ Tue, 02 Aug 2022 10:31:22: #2 finished! INFO @ Tue, 02 Aug 2022 10:31:22: #2 predicted fragment length is 144 bps INFO @ Tue, 02 Aug 2022 10:31:22: #2 alternative fragment length(s) may be 144 bps INFO @ Tue, 02 Aug 2022 10:31:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435537/SRX10435537.10_model.r WARNING @ Tue, 02 Aug 2022 10:31:22: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:31:22: #2 You may need to consider one of the other alternative d(s): 144 WARNING @ Tue, 02 Aug 2022 10:31:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:31:22: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:31:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:31:26: 4000000 INFO @ Tue, 02 Aug 2022 10:31:35: 5000000 INFO @ Tue, 02 Aug 2022 10:31:40: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:31:44: 6000000 INFO @ Tue, 02 Aug 2022 10:31:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435537/SRX10435537.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:31:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435537/SRX10435537.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:31:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435537/SRX10435537.10_summits.bed INFO @ Tue, 02 Aug 2022 10:31:49: Done! pass1 - making usageList (7 chroms): 6 millis pass2 - checking and writing primary data (1417 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:31:53: 7000000 INFO @ Tue, 02 Aug 2022 10:32:03: 8000000 INFO @ Tue, 02 Aug 2022 10:32:05: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:32:05: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:32:05: #1 total tags in treatment: 8207030 INFO @ Tue, 02 Aug 2022 10:32:05: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:32:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:32:05: #1 tags after filtering in treatment: 8207030 INFO @ Tue, 02 Aug 2022 10:32:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:32:05: #1 finished! INFO @ Tue, 02 Aug 2022 10:32:05: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:32:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:32:06: #2 number of paired peaks: 694 WARNING @ Tue, 02 Aug 2022 10:32:06: Fewer paired peaks (694) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 694 pairs to build model! INFO @ Tue, 02 Aug 2022 10:32:06: start model_add_line... INFO @ Tue, 02 Aug 2022 10:32:06: start X-correlation... INFO @ Tue, 02 Aug 2022 10:32:06: end of X-cor INFO @ Tue, 02 Aug 2022 10:32:06: #2 finished! INFO @ Tue, 02 Aug 2022 10:32:06: #2 predicted fragment length is 144 bps INFO @ Tue, 02 Aug 2022 10:32:06: #2 alternative fragment length(s) may be 144 bps INFO @ Tue, 02 Aug 2022 10:32:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435537/SRX10435537.20_model.r WARNING @ Tue, 02 Aug 2022 10:32:06: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:32:06: #2 You may need to consider one of the other alternative d(s): 144 WARNING @ Tue, 02 Aug 2022 10:32:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:32:06: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:32:06: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:32:25: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:32:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435537/SRX10435537.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:32:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435537/SRX10435537.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:32:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435537/SRX10435537.20_summits.bed INFO @ Tue, 02 Aug 2022 10:32:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (810 records, 4 fields): 26 millis CompletedMACS2peakCalling BigWig に変換しました。