Job ID = 16434974 SRX = SRX10435539 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 9899363 spots for SRR14060955/SRR14060955.sra Written 9899363 spots for SRR14060955/SRR14060955.sra fastq に変換しました。 bowtie でマッピング中... Your job 16435012 ("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: 00:02:21 9899363 reads; of these: 9899363 (100.00%) were unpaired; of these: 141468 (1.43%) aligned 0 times 8209209 (82.93%) aligned exactly 1 time 1548686 (15.64%) aligned >1 times 98.57% overall alignment rate Time searching: 00:02:21 Overall time: 00:02:21 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] 658482 / 9757895 = 0.0675 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 10:29:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435539/SRX10435539.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435539/SRX10435539.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435539/SRX10435539.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435539/SRX10435539.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 10:29:03: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:29:03: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:29:09: 1000000 INFO @ Tue, 02 Aug 2022 10:29:15: 2000000 INFO @ Tue, 02 Aug 2022 10:29:21: 3000000 INFO @ Tue, 02 Aug 2022 10:29:27: 4000000 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 10:29:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435539/SRX10435539.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435539/SRX10435539.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435539/SRX10435539.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435539/SRX10435539.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 10:29:33: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:29:33: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:29:34: 5000000 INFO @ Tue, 02 Aug 2022 10:29:39: 1000000 INFO @ Tue, 02 Aug 2022 10:29:41: 6000000 INFO @ Tue, 02 Aug 2022 10:29:46: 2000000 INFO @ Tue, 02 Aug 2022 10:29:47: 7000000 INFO @ Tue, 02 Aug 2022 10:29:53: 3000000 INFO @ Tue, 02 Aug 2022 10:29:54: 8000000 INFO @ Tue, 02 Aug 2022 10:30:00: 4000000 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 10:30:01: 9000000 INFO @ Tue, 02 Aug 2022 10:30:02: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 10:30:02: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 10:30:02: #1 total tags in treatment: 9099413 INFO @ Tue, 02 Aug 2022 10:30:02: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:30:02: #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 10:30:02: #1 tags after filtering in treatment: 9099413 INFO @ Tue, 02 Aug 2022 10:30:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:30:02: #1 finished! INFO @ Tue, 02 Aug 2022 10:30:02: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:30:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:30:02: #2 number of paired peaks: 287 WARNING @ Tue, 02 Aug 2022 10:30:02: Fewer paired peaks (287) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 287 pairs to build model! INFO @ Tue, 02 Aug 2022 10:30:02: start model_add_line... INFO @ Tue, 02 Aug 2022 10:30:02: start X-correlation... INFO @ Tue, 02 Aug 2022 10:30:02: end of X-cor INFO @ Tue, 02 Aug 2022 10:30:02: #2 finished! INFO @ Tue, 02 Aug 2022 10:30:02: #2 predicted fragment length is 53 bps INFO @ Tue, 02 Aug 2022 10:30:02: #2 alternative fragment length(s) may be 4,53 bps INFO @ Tue, 02 Aug 2022 10:30:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435539/SRX10435539.05_model.r WARNING @ Tue, 02 Aug 2022 10:30:02: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:30:02: #2 You may need to consider one of the other alternative d(s): 4,53 WARNING @ Tue, 02 Aug 2022 10:30:02: #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 10:30:02: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:30:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:30:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435539/SRX10435539.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435539/SRX10435539.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435539/SRX10435539.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435539/SRX10435539.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 10:30:03: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:30:03: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:30:07: 5000000 INFO @ Tue, 02 Aug 2022 10:30:09: 1000000 INFO @ Tue, 02 Aug 2022 10:30:14: 6000000 INFO @ Tue, 02 Aug 2022 10:30:15: 2000000 INFO @ Tue, 02 Aug 2022 10:30:20: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:30:21: 7000000 INFO @ Tue, 02 Aug 2022 10:30:21: 3000000 INFO @ Tue, 02 Aug 2022 10:30:27: 4000000 INFO @ Tue, 02 Aug 2022 10:30:27: 8000000 INFO @ Tue, 02 Aug 2022 10:30:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435539/SRX10435539.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:30:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435539/SRX10435539.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:30:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435539/SRX10435539.05_summits.bed INFO @ Tue, 02 Aug 2022 10:30:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (540 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:30:33: 5000000 INFO @ Tue, 02 Aug 2022 10:30:34: 9000000 INFO @ Tue, 02 Aug 2022 10:30:35: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 10:30:35: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 10:30:35: #1 total tags in treatment: 9099413 INFO @ Tue, 02 Aug 2022 10:30:35: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:30:35: #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 10:30:35: #1 tags after filtering in treatment: 9099413 INFO @ Tue, 02 Aug 2022 10:30:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:30:35: #1 finished! INFO @ Tue, 02 Aug 2022 10:30:35: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:30:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:30:35: #2 number of paired peaks: 287 WARNING @ Tue, 02 Aug 2022 10:30:35: Fewer paired peaks (287) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 287 pairs to build model! INFO @ Tue, 02 Aug 2022 10:30:35: start model_add_line... INFO @ Tue, 02 Aug 2022 10:30:36: start X-correlation... INFO @ Tue, 02 Aug 2022 10:30:36: end of X-cor INFO @ Tue, 02 Aug 2022 10:30:36: #2 finished! INFO @ Tue, 02 Aug 2022 10:30:36: #2 predicted fragment length is 53 bps INFO @ Tue, 02 Aug 2022 10:30:36: #2 alternative fragment length(s) may be 4,53 bps INFO @ Tue, 02 Aug 2022 10:30:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435539/SRX10435539.10_model.r WARNING @ Tue, 02 Aug 2022 10:30:36: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:30:36: #2 You may need to consider one of the other alternative d(s): 4,53 WARNING @ Tue, 02 Aug 2022 10:30:36: #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 10:30:36: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:30:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:30:39: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:30:45: 7000000 INFO @ Tue, 02 Aug 2022 10:30:50: 8000000 INFO @ Tue, 02 Aug 2022 10:30:54: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:30:55: 9000000 INFO @ Tue, 02 Aug 2022 10:30:56: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 10:30:56: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 10:30:56: #1 total tags in treatment: 9099413 INFO @ Tue, 02 Aug 2022 10:30:56: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:30:56: #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 10:30:56: #1 tags after filtering in treatment: 9099413 INFO @ Tue, 02 Aug 2022 10:30:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:30:56: #1 finished! INFO @ Tue, 02 Aug 2022 10:30:56: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:30:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:30:56: #2 number of paired peaks: 287 WARNING @ Tue, 02 Aug 2022 10:30:56: Fewer paired peaks (287) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 287 pairs to build model! INFO @ Tue, 02 Aug 2022 10:30:56: start model_add_line... INFO @ Tue, 02 Aug 2022 10:30:56: start X-correlation... INFO @ Tue, 02 Aug 2022 10:30:56: end of X-cor INFO @ Tue, 02 Aug 2022 10:30:56: #2 finished! INFO @ Tue, 02 Aug 2022 10:30:56: #2 predicted fragment length is 53 bps INFO @ Tue, 02 Aug 2022 10:30:56: #2 alternative fragment length(s) may be 4,53 bps INFO @ Tue, 02 Aug 2022 10:30:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435539/SRX10435539.20_model.r WARNING @ Tue, 02 Aug 2022 10:30:56: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:30:56: #2 You may need to consider one of the other alternative d(s): 4,53 WARNING @ Tue, 02 Aug 2022 10:30:56: #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 10:30:56: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:30:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:31:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435539/SRX10435539.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:31:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435539/SRX10435539.10_peaks.narrowPeak BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:31:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435539/SRX10435539.10_summits.bed INFO @ Tue, 02 Aug 2022 10:31:03: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (315 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:31:14: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:31:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435539/SRX10435539.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:31:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435539/SRX10435539.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:31:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435539/SRX10435539.20_summits.bed INFO @ Tue, 02 Aug 2022 10:31:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (130 records, 4 fields): 1 millis CompletedMACS2peakCalling