Job ID = 16434943 SRX = SRX11633399 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 9495874 spots for SRR15329108/SRR15329108.sra Written 9495874 spots for SRR15329108/SRR15329108.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434981 ("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: 00:03:16 9495874 reads; of these: 9495874 (100.00%) were unpaired; of these: 495408 (5.22%) aligned 0 times 7732075 (81.43%) aligned exactly 1 time 1268391 (13.36%) aligned >1 times 94.78% overall alignment rate Time searching: 00:03:16 Overall time: 00:03:16 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] 505156 / 9000466 = 0.0561 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 10:25:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11633399/SRX11633399.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11633399/SRX11633399.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11633399/SRX11633399.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11633399/SRX11633399.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 10:25:34: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:25:34: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:25:41: 1000000 INFO @ Tue, 02 Aug 2022 10:25:47: 2000000 INFO @ Tue, 02 Aug 2022 10:25:53: 3000000 INFO @ Tue, 02 Aug 2022 10:25:59: 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 10:26:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11633399/SRX11633399.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11633399/SRX11633399.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11633399/SRX11633399.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11633399/SRX11633399.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 10:26:04: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:26:04: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:26:05: 5000000 INFO @ Tue, 02 Aug 2022 10:26:11: 1000000 INFO @ Tue, 02 Aug 2022 10:26:12: 6000000 INFO @ Tue, 02 Aug 2022 10:26:18: 2000000 INFO @ Tue, 02 Aug 2022 10:26:19: 7000000 INFO @ Tue, 02 Aug 2022 10:26:25: 3000000 INFO @ Tue, 02 Aug 2022 10:26:26: 8000000 INFO @ Tue, 02 Aug 2022 10:26:29: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:26:29: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:26:29: #1 total tags in treatment: 8495310 INFO @ Tue, 02 Aug 2022 10:26:29: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:26:29: #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 10:26:29: #1 tags after filtering in treatment: 8495310 INFO @ Tue, 02 Aug 2022 10:26:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:26:29: #1 finished! INFO @ Tue, 02 Aug 2022 10:26:29: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:26:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:26:30: #2 number of paired peaks: 236 WARNING @ Tue, 02 Aug 2022 10:26:30: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Tue, 02 Aug 2022 10:26:30: start model_add_line... INFO @ Tue, 02 Aug 2022 10:26:30: start X-correlation... INFO @ Tue, 02 Aug 2022 10:26:30: end of X-cor INFO @ Tue, 02 Aug 2022 10:26:30: #2 finished! INFO @ Tue, 02 Aug 2022 10:26:30: #2 predicted fragment length is 70 bps INFO @ Tue, 02 Aug 2022 10:26:30: #2 alternative fragment length(s) may be 4,70 bps INFO @ Tue, 02 Aug 2022 10:26:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11633399/SRX11633399.05_model.r WARNING @ Tue, 02 Aug 2022 10:26:30: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:26:30: #2 You may need to consider one of the other alternative d(s): 4,70 WARNING @ Tue, 02 Aug 2022 10:26:30: #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 10:26:30: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:26:30: #3 Pre-compute pvalue-qvalue table... 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 10:26:32: 4000000 INFO @ Tue, 02 Aug 2022 10:26:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11633399/SRX11633399.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11633399/SRX11633399.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11633399/SRX11633399.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11633399/SRX11633399.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 10:26:34: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:26:34: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:26:39: 5000000 INFO @ Tue, 02 Aug 2022 10:26:41: 1000000 INFO @ Tue, 02 Aug 2022 10:26:46: 6000000 INFO @ Tue, 02 Aug 2022 10:26:47: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:26:48: 2000000 INFO @ Tue, 02 Aug 2022 10:26:53: 7000000 INFO @ Tue, 02 Aug 2022 10:26:55: 3000000 INFO @ Tue, 02 Aug 2022 10:26:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11633399/SRX11633399.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:26:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11633399/SRX11633399.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:26:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11633399/SRX11633399.05_summits.bed INFO @ Tue, 02 Aug 2022 10:26:56: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (432 records, 4 fields): 67 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:26:59: 8000000 INFO @ Tue, 02 Aug 2022 10:27:02: 4000000 INFO @ Tue, 02 Aug 2022 10:27:03: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:27:03: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:27:03: #1 total tags in treatment: 8495310 INFO @ Tue, 02 Aug 2022 10:27:03: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:27:03: #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 10:27:03: #1 tags after filtering in treatment: 8495310 INFO @ Tue, 02 Aug 2022 10:27:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:27:03: #1 finished! INFO @ Tue, 02 Aug 2022 10:27:03: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:27:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:27:04: #2 number of paired peaks: 236 WARNING @ Tue, 02 Aug 2022 10:27:04: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Tue, 02 Aug 2022 10:27:04: start model_add_line... INFO @ Tue, 02 Aug 2022 10:27:04: start X-correlation... INFO @ Tue, 02 Aug 2022 10:27:04: end of X-cor INFO @ Tue, 02 Aug 2022 10:27:04: #2 finished! INFO @ Tue, 02 Aug 2022 10:27:04: #2 predicted fragment length is 70 bps INFO @ Tue, 02 Aug 2022 10:27:04: #2 alternative fragment length(s) may be 4,70 bps INFO @ Tue, 02 Aug 2022 10:27:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11633399/SRX11633399.10_model.r WARNING @ Tue, 02 Aug 2022 10:27:04: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:27:04: #2 You may need to consider one of the other alternative d(s): 4,70 WARNING @ Tue, 02 Aug 2022 10:27:04: #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 10:27:04: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:27:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:27:09: 5000000 INFO @ Tue, 02 Aug 2022 10:27:15: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:27:21: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:27:21: 7000000 INFO @ Tue, 02 Aug 2022 10:27:27: 8000000 INFO @ Tue, 02 Aug 2022 10:27:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11633399/SRX11633399.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:27:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11633399/SRX11633399.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:27:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11633399/SRX11633399.10_summits.bed INFO @ Tue, 02 Aug 2022 10:27:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (274 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:27:30: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:27:30: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:27:30: #1 total tags in treatment: 8495310 INFO @ Tue, 02 Aug 2022 10:27:30: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:27:30: #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 10:27:30: #1 tags after filtering in treatment: 8495310 INFO @ Tue, 02 Aug 2022 10:27:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:27:30: #1 finished! INFO @ Tue, 02 Aug 2022 10:27:30: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:27:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:27:30: #2 number of paired peaks: 236 WARNING @ Tue, 02 Aug 2022 10:27:30: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Tue, 02 Aug 2022 10:27:30: start model_add_line... INFO @ Tue, 02 Aug 2022 10:27:30: start X-correlation... INFO @ Tue, 02 Aug 2022 10:27:31: end of X-cor INFO @ Tue, 02 Aug 2022 10:27:31: #2 finished! INFO @ Tue, 02 Aug 2022 10:27:31: #2 predicted fragment length is 70 bps INFO @ Tue, 02 Aug 2022 10:27:31: #2 alternative fragment length(s) may be 4,70 bps INFO @ Tue, 02 Aug 2022 10:27:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11633399/SRX11633399.20_model.r WARNING @ Tue, 02 Aug 2022 10:27:31: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:27:31: #2 You may need to consider one of the other alternative d(s): 4,70 WARNING @ Tue, 02 Aug 2022 10:27:31: #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 10:27:31: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:27:31: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:27:47: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:27:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11633399/SRX11633399.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:27:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11633399/SRX11633399.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:27:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11633399/SRX11633399.20_summits.bed INFO @ Tue, 02 Aug 2022 10:27:56: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (154 records, 4 fields): 17 millis CompletedMACS2peakCalling