Job ID = 16434944 SRX = SRX10435530 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 15548551 spots for SRR14060930/SRR14060930.sra Written 15548551 spots for SRR14060930/SRR14060930.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434984 ("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: 00:02:58 15548551 reads; of these: 15548551 (100.00%) were unpaired; of these: 3765369 (24.22%) aligned 0 times 9934247 (63.89%) aligned exactly 1 time 1848935 (11.89%) aligned >1 times 75.78% overall alignment rate Time searching: 00:02:58 Overall time: 00:02:58 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_sort_core] merging from 8 files... [bam_rmdupse_core] 2948938 / 11783182 = 0.2503 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 10:24:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435530/SRX10435530.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435530/SRX10435530.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435530/SRX10435530.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435530/SRX10435530.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 10:24:49: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:24:49: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:24:54: 1000000 INFO @ Tue, 02 Aug 2022 10:24:59: 2000000 INFO @ Tue, 02 Aug 2022 10:25:04: 3000000 INFO @ Tue, 02 Aug 2022 10:25:10: 4000000 INFO @ Tue, 02 Aug 2022 10:25:15: 5000000 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 10:25:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435530/SRX10435530.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435530/SRX10435530.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435530/SRX10435530.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435530/SRX10435530.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 10:25:19: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:25:19: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:25:20: 6000000 INFO @ Tue, 02 Aug 2022 10:25:24: 1000000 INFO @ Tue, 02 Aug 2022 10:25:26: 7000000 INFO @ Tue, 02 Aug 2022 10:25:30: 2000000 INFO @ Tue, 02 Aug 2022 10:25:31: 8000000 INFO @ Tue, 02 Aug 2022 10:25:35: 3000000 INFO @ Tue, 02 Aug 2022 10:25:36: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 10:25:36: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 10:25:36: #1 total tags in treatment: 8834244 INFO @ Tue, 02 Aug 2022 10:25:36: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:25:36: #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 10:25:36: #1 tags after filtering in treatment: 8834244 INFO @ Tue, 02 Aug 2022 10:25:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:25:36: #1 finished! INFO @ Tue, 02 Aug 2022 10:25:36: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:25:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:25:37: #2 number of paired peaks: 657 WARNING @ Tue, 02 Aug 2022 10:25:37: Fewer paired peaks (657) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 657 pairs to build model! INFO @ Tue, 02 Aug 2022 10:25:37: start model_add_line... INFO @ Tue, 02 Aug 2022 10:25:37: start X-correlation... INFO @ Tue, 02 Aug 2022 10:25:37: end of X-cor INFO @ Tue, 02 Aug 2022 10:25:37: #2 finished! INFO @ Tue, 02 Aug 2022 10:25:37: #2 predicted fragment length is 140 bps INFO @ Tue, 02 Aug 2022 10:25:37: #2 alternative fragment length(s) may be 140 bps INFO @ Tue, 02 Aug 2022 10:25:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435530/SRX10435530.05_model.r INFO @ Tue, 02 Aug 2022 10:25:37: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:25:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:25:41: 4000000 INFO @ Tue, 02 Aug 2022 10:25:46: 5000000 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 10:25:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435530/SRX10435530.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435530/SRX10435530.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435530/SRX10435530.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435530/SRX10435530.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 10:25:49: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:25:49: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:25:51: 6000000 INFO @ Tue, 02 Aug 2022 10:25:55: 1000000 INFO @ Tue, 02 Aug 2022 10:25:56: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:25:57: 7000000 INFO @ Tue, 02 Aug 2022 10:26:01: 2000000 INFO @ Tue, 02 Aug 2022 10:26:02: 8000000 INFO @ Tue, 02 Aug 2022 10:26:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435530/SRX10435530.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:26:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435530/SRX10435530.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:26:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435530/SRX10435530.05_summits.bed INFO @ Tue, 02 Aug 2022 10:26:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1601 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:26:06: 3000000 INFO @ Tue, 02 Aug 2022 10:26:06: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 10:26:06: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 10:26:06: #1 total tags in treatment: 8834244 INFO @ Tue, 02 Aug 2022 10:26:06: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:26:06: #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 10:26:07: #1 tags after filtering in treatment: 8834244 INFO @ Tue, 02 Aug 2022 10:26:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:26:07: #1 finished! INFO @ Tue, 02 Aug 2022 10:26:07: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:26:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:26:07: #2 number of paired peaks: 657 WARNING @ Tue, 02 Aug 2022 10:26:07: Fewer paired peaks (657) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 657 pairs to build model! INFO @ Tue, 02 Aug 2022 10:26:07: start model_add_line... INFO @ Tue, 02 Aug 2022 10:26:07: start X-correlation... INFO @ Tue, 02 Aug 2022 10:26:07: end of X-cor INFO @ Tue, 02 Aug 2022 10:26:07: #2 finished! INFO @ Tue, 02 Aug 2022 10:26:07: #2 predicted fragment length is 140 bps INFO @ Tue, 02 Aug 2022 10:26:07: #2 alternative fragment length(s) may be 140 bps INFO @ Tue, 02 Aug 2022 10:26:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435530/SRX10435530.10_model.r INFO @ Tue, 02 Aug 2022 10:26:07: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:26:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:26:11: 4000000 INFO @ Tue, 02 Aug 2022 10:26:16: 5000000 INFO @ Tue, 02 Aug 2022 10:26:22: 6000000 INFO @ Tue, 02 Aug 2022 10:26:26: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:26:27: 7000000 INFO @ Tue, 02 Aug 2022 10:26:32: 8000000 INFO @ Tue, 02 Aug 2022 10:26:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435530/SRX10435530.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:26:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435530/SRX10435530.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:26:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435530/SRX10435530.10_summits.bed INFO @ Tue, 02 Aug 2022 10:26:36: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 10:26:36: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 10:26:36: #1 total tags in treatment: 8834244 INFO @ Tue, 02 Aug 2022 10:26:36: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:26:36: #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 10:26:36: Done! INFO @ Tue, 02 Aug 2022 10:26:36: #1 tags after filtering in treatment: 8834244 INFO @ Tue, 02 Aug 2022 10:26:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:26:36: #1 finished! INFO @ Tue, 02 Aug 2022 10:26:36: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:26:36: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1073 records, 4 fields): 90 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:26:37: #2 number of paired peaks: 657 WARNING @ Tue, 02 Aug 2022 10:26:37: Fewer paired peaks (657) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 657 pairs to build model! INFO @ Tue, 02 Aug 2022 10:26:37: start model_add_line... INFO @ Tue, 02 Aug 2022 10:26:37: start X-correlation... INFO @ Tue, 02 Aug 2022 10:26:37: end of X-cor INFO @ Tue, 02 Aug 2022 10:26:37: #2 finished! INFO @ Tue, 02 Aug 2022 10:26:37: #2 predicted fragment length is 140 bps INFO @ Tue, 02 Aug 2022 10:26:37: #2 alternative fragment length(s) may be 140 bps INFO @ Tue, 02 Aug 2022 10:26:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435530/SRX10435530.20_model.r INFO @ Tue, 02 Aug 2022 10:26:37: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:26:37: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:26:56: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:27:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435530/SRX10435530.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:27:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435530/SRX10435530.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:27:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435530/SRX10435530.20_summits.bed INFO @ Tue, 02 Aug 2022 10:27:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (652 records, 4 fields): 14 millis CompletedMACS2peakCalling