Job ID = 10165667 SRX = SRX8331145 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 10743677 spots for SRR11778458/SRR11778458.sra Written 10743677 spots for SRR11778458/SRR11778458.sra fastq に変換しました。 bowtie でマッピング中... Your job 10165804 ("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: 00:03:43 10743677 reads; of these: 10743677 (100.00%) were unpaired; of these: 1610326 (14.99%) aligned 0 times 7229921 (67.29%) aligned exactly 1 time 1903430 (17.72%) aligned >1 times 85.01% overall alignment rate Time searching: 00:03:43 Overall time: 00:03:43 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] 8521402 / 9133351 = 0.9330 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 19:39:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8331145/SRX8331145.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8331145/SRX8331145.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8331145/SRX8331145.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8331145/SRX8331145.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 19:39:22: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:39:22: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:39:25: #1 tag size is determined as 61 bps INFO @ Thu, 08 Oct 2020 19:39:25: #1 tag size = 61 INFO @ Thu, 08 Oct 2020 19:39:25: #1 total tags in treatment: 611949 INFO @ Thu, 08 Oct 2020 19:39:25: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:39:25: #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 19:39:25: #1 tags after filtering in treatment: 611949 INFO @ Thu, 08 Oct 2020 19:39:25: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:39:25: #1 finished! INFO @ Thu, 08 Oct 2020 19:39:25: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:39:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:39:26: #2 number of paired peaks: 1772 INFO @ Thu, 08 Oct 2020 19:39:26: start model_add_line... INFO @ Thu, 08 Oct 2020 19:39:26: start X-correlation... INFO @ Thu, 08 Oct 2020 19:39:26: end of X-cor INFO @ Thu, 08 Oct 2020 19:39:26: #2 finished! INFO @ Thu, 08 Oct 2020 19:39:26: #2 predicted fragment length is 65 bps INFO @ Thu, 08 Oct 2020 19:39:26: #2 alternative fragment length(s) may be 65 bps INFO @ Thu, 08 Oct 2020 19:39:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8331145/SRX8331145.05_model.r WARNING @ Thu, 08 Oct 2020 19:39:26: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:39:26: #2 You may need to consider one of the other alternative d(s): 65 WARNING @ Thu, 08 Oct 2020 19:39:26: #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 19:39:26: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:39:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:39:27: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:39:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8331145/SRX8331145.05_peaks.xls INFO @ Thu, 08 Oct 2020 19:39:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8331145/SRX8331145.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:39:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8331145/SRX8331145.05_summits.bed INFO @ Thu, 08 Oct 2020 19:39:28: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (756 records, 4 fields): 3 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 @ Thu, 08 Oct 2020 19:39:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8331145/SRX8331145.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8331145/SRX8331145.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8331145/SRX8331145.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8331145/SRX8331145.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 19:39:51: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:39:51: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:39:55: #1 tag size is determined as 61 bps INFO @ Thu, 08 Oct 2020 19:39:55: #1 tag size = 61 INFO @ Thu, 08 Oct 2020 19:39:55: #1 total tags in treatment: 611949 INFO @ Thu, 08 Oct 2020 19:39:55: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:39:55: #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 19:39:55: #1 tags after filtering in treatment: 611949 INFO @ Thu, 08 Oct 2020 19:39:55: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:39:55: #1 finished! INFO @ Thu, 08 Oct 2020 19:39:55: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:39:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:39:55: #2 number of paired peaks: 1772 INFO @ Thu, 08 Oct 2020 19:39:55: start model_add_line... INFO @ Thu, 08 Oct 2020 19:39:55: start X-correlation... INFO @ Thu, 08 Oct 2020 19:39:55: end of X-cor INFO @ Thu, 08 Oct 2020 19:39:55: #2 finished! INFO @ Thu, 08 Oct 2020 19:39:55: #2 predicted fragment length is 65 bps INFO @ Thu, 08 Oct 2020 19:39:55: #2 alternative fragment length(s) may be 65 bps INFO @ Thu, 08 Oct 2020 19:39:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8331145/SRX8331145.10_model.r WARNING @ Thu, 08 Oct 2020 19:39:55: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:39:55: #2 You may need to consider one of the other alternative d(s): 65 WARNING @ Thu, 08 Oct 2020 19:39:55: #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 19:39:55: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:39:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:39:57: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:39:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8331145/SRX8331145.10_peaks.xls INFO @ Thu, 08 Oct 2020 19:39:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8331145/SRX8331145.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:39:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8331145/SRX8331145.10_summits.bed INFO @ Thu, 08 Oct 2020 19:39:58: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (406 records, 4 fields): 2 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 @ Thu, 08 Oct 2020 19:40:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8331145/SRX8331145.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8331145/SRX8331145.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8331145/SRX8331145.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8331145/SRX8331145.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 19:40:21: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:40:21: #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 @ Thu, 08 Oct 2020 19:40:24: #1 tag size is determined as 61 bps INFO @ Thu, 08 Oct 2020 19:40:24: #1 tag size = 61 INFO @ Thu, 08 Oct 2020 19:40:24: #1 total tags in treatment: 611949 INFO @ Thu, 08 Oct 2020 19:40:24: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:40:24: #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 19:40:24: #1 tags after filtering in treatment: 611949 INFO @ Thu, 08 Oct 2020 19:40:24: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:40:24: #1 finished! INFO @ Thu, 08 Oct 2020 19:40:24: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:40:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:40:25: #2 number of paired peaks: 1772 INFO @ Thu, 08 Oct 2020 19:40:25: start model_add_line... INFO @ Thu, 08 Oct 2020 19:40:25: start X-correlation... INFO @ Thu, 08 Oct 2020 19:40:25: end of X-cor INFO @ Thu, 08 Oct 2020 19:40:25: #2 finished! INFO @ Thu, 08 Oct 2020 19:40:25: #2 predicted fragment length is 65 bps INFO @ Thu, 08 Oct 2020 19:40:25: #2 alternative fragment length(s) may be 65 bps INFO @ Thu, 08 Oct 2020 19:40:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8331145/SRX8331145.20_model.r WARNING @ Thu, 08 Oct 2020 19:40:25: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:40:25: #2 You may need to consider one of the other alternative d(s): 65 WARNING @ Thu, 08 Oct 2020 19:40:25: #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 19:40:25: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:40:25: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:40:26: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:40:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8331145/SRX8331145.20_peaks.xls INFO @ Thu, 08 Oct 2020 19:40:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8331145/SRX8331145.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:40:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8331145/SRX8331145.20_summits.bed INFO @ Thu, 08 Oct 2020 19:40:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (190 records, 4 fields): 1 millis CompletedMACS2peakCalling