Job ID = 16434946 SRX = SRX10435531 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 14873708 spots for SRR14060931/SRR14060931.sra Written 14873708 spots for SRR14060931/SRR14060931.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434990 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:03:17 14873708 reads; of these: 14873708 (100.00%) were unpaired; of these: 3068452 (20.63%) aligned 0 times 10009968 (67.30%) aligned exactly 1 time 1795288 (12.07%) aligned >1 times 79.37% overall alignment rate Time searching: 00:03:18 Overall time: 00:03:18 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] 1881326 / 11805256 = 0.1594 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 10:27:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435531/SRX10435531.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435531/SRX10435531.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435531/SRX10435531.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435531/SRX10435531.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 10:27:25: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:27:25: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:27:34: 1000000 INFO @ Tue, 02 Aug 2022 10:27:43: 2000000 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 10:27:52: 3000000 INFO @ Tue, 02 Aug 2022 10:27:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435531/SRX10435531.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435531/SRX10435531.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435531/SRX10435531.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435531/SRX10435531.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 10:27:54: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:27:54: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:28:01: 4000000 INFO @ Tue, 02 Aug 2022 10:28:02: 1000000 INFO @ Tue, 02 Aug 2022 10:28:09: 2000000 INFO @ Tue, 02 Aug 2022 10:28:11: 5000000 INFO @ Tue, 02 Aug 2022 10:28:16: 3000000 INFO @ Tue, 02 Aug 2022 10:28:20: 6000000 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 10:28:24: 4000000 INFO @ Tue, 02 Aug 2022 10:28:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435531/SRX10435531.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435531/SRX10435531.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435531/SRX10435531.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435531/SRX10435531.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 10:28:24: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:28:24: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:28:29: 7000000 INFO @ Tue, 02 Aug 2022 10:28:31: 5000000 INFO @ Tue, 02 Aug 2022 10:28:34: 1000000 INFO @ Tue, 02 Aug 2022 10:28:39: 8000000 INFO @ Tue, 02 Aug 2022 10:28:39: 6000000 INFO @ Tue, 02 Aug 2022 10:28:43: 2000000 INFO @ Tue, 02 Aug 2022 10:28:46: 7000000 INFO @ Tue, 02 Aug 2022 10:28:48: 9000000 INFO @ Tue, 02 Aug 2022 10:28:53: 3000000 INFO @ Tue, 02 Aug 2022 10:28:53: 8000000 INFO @ Tue, 02 Aug 2022 10:28:57: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 10:28:57: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 10:28:57: #1 total tags in treatment: 9923930 INFO @ Tue, 02 Aug 2022 10:28:57: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:28:57: #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 10:28:57: #1 tags after filtering in treatment: 9923930 INFO @ Tue, 02 Aug 2022 10:28:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:28:57: #1 finished! INFO @ Tue, 02 Aug 2022 10:28:57: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:28:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:28:58: #2 number of paired peaks: 726 WARNING @ Tue, 02 Aug 2022 10:28:58: Fewer paired peaks (726) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 726 pairs to build model! INFO @ Tue, 02 Aug 2022 10:28:58: start model_add_line... INFO @ Tue, 02 Aug 2022 10:28:58: start X-correlation... INFO @ Tue, 02 Aug 2022 10:28:58: end of X-cor INFO @ Tue, 02 Aug 2022 10:28:58: #2 finished! INFO @ Tue, 02 Aug 2022 10:28:58: #2 predicted fragment length is 159 bps INFO @ Tue, 02 Aug 2022 10:28:58: #2 alternative fragment length(s) may be 159 bps INFO @ Tue, 02 Aug 2022 10:28:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435531/SRX10435531.05_model.r INFO @ Tue, 02 Aug 2022 10:28:58: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:28:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:29:00: 9000000 INFO @ Tue, 02 Aug 2022 10:29:02: 4000000 INFO @ Tue, 02 Aug 2022 10:29:07: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 10:29:07: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 10:29:07: #1 total tags in treatment: 9923930 INFO @ Tue, 02 Aug 2022 10:29:07: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:29:07: #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 10:29:07: #1 tags after filtering in treatment: 9923930 INFO @ Tue, 02 Aug 2022 10:29:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:29:07: #1 finished! INFO @ Tue, 02 Aug 2022 10:29:07: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:29:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:29:08: #2 number of paired peaks: 726 WARNING @ Tue, 02 Aug 2022 10:29:08: Fewer paired peaks (726) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 726 pairs to build model! INFO @ Tue, 02 Aug 2022 10:29:08: start model_add_line... INFO @ Tue, 02 Aug 2022 10:29:08: start X-correlation... INFO @ Tue, 02 Aug 2022 10:29:08: end of X-cor INFO @ Tue, 02 Aug 2022 10:29:08: #2 finished! INFO @ Tue, 02 Aug 2022 10:29:08: #2 predicted fragment length is 159 bps INFO @ Tue, 02 Aug 2022 10:29:08: #2 alternative fragment length(s) may be 159 bps INFO @ Tue, 02 Aug 2022 10:29:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435531/SRX10435531.10_model.r INFO @ Tue, 02 Aug 2022 10:29:08: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:29:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:29:12: 5000000 INFO @ Tue, 02 Aug 2022 10:29:20: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:29:22: 6000000 INFO @ Tue, 02 Aug 2022 10:29:29: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:29:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435531/SRX10435531.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:29:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435531/SRX10435531.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:29:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435531/SRX10435531.05_summits.bed INFO @ Tue, 02 Aug 2022 10:29:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2328 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:29:31: 7000000 INFO @ Tue, 02 Aug 2022 10:29:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435531/SRX10435531.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:29:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435531/SRX10435531.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:29:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435531/SRX10435531.10_summits.bed INFO @ Tue, 02 Aug 2022 10:29:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1480 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:29:40: 8000000 INFO @ Tue, 02 Aug 2022 10:29:49: 9000000 INFO @ Tue, 02 Aug 2022 10:29:58: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 10:29:58: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 10:29:58: #1 total tags in treatment: 9923930 INFO @ Tue, 02 Aug 2022 10:29:58: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:29:58: #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 10:29:58: #1 tags after filtering in treatment: 9923930 INFO @ Tue, 02 Aug 2022 10:29:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:29:58: #1 finished! INFO @ Tue, 02 Aug 2022 10:29:58: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:29:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:29:59: #2 number of paired peaks: 726 WARNING @ Tue, 02 Aug 2022 10:29:59: Fewer paired peaks (726) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 726 pairs to build model! INFO @ Tue, 02 Aug 2022 10:29:59: start model_add_line... INFO @ Tue, 02 Aug 2022 10:29:59: start X-correlation... INFO @ Tue, 02 Aug 2022 10:29:59: end of X-cor INFO @ Tue, 02 Aug 2022 10:29:59: #2 finished! INFO @ Tue, 02 Aug 2022 10:29:59: #2 predicted fragment length is 159 bps INFO @ Tue, 02 Aug 2022 10:29:59: #2 alternative fragment length(s) may be 159 bps INFO @ Tue, 02 Aug 2022 10:29:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435531/SRX10435531.20_model.r INFO @ Tue, 02 Aug 2022 10:29:59: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:29:59: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:30:22: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:30:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435531/SRX10435531.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:30:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435531/SRX10435531.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:30:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435531/SRX10435531.20_summits.bed INFO @ Tue, 02 Aug 2022 10:30:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (882 records, 4 fields): 65 millis CompletedMACS2peakCalling