Job ID = 14158799 SRX = SRX7665444 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:23 15470898 reads; of these: 15470898 (100.00%) were unpaired; of these: 803676 (5.19%) aligned 0 times 12064262 (77.98%) aligned exactly 1 time 2602960 (16.82%) aligned >1 times 94.81% overall alignment rate Time searching: 00:02:23 Overall time: 00:02:23 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] 2194250 / 14667222 = 0.1496 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 18:05:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7665444/SRX7665444.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7665444/SRX7665444.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7665444/SRX7665444.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7665444/SRX7665444.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 @ Wed, 08 Dec 2021 18:05:11: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:05:11: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:05:15: 1000000 INFO @ Wed, 08 Dec 2021 18:05:20: 2000000 INFO @ Wed, 08 Dec 2021 18:05:25: 3000000 INFO @ Wed, 08 Dec 2021 18:05:29: 4000000 INFO @ Wed, 08 Dec 2021 18:05:34: 5000000 INFO @ Wed, 08 Dec 2021 18:05:39: 6000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 18:05:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7665444/SRX7665444.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7665444/SRX7665444.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7665444/SRX7665444.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7665444/SRX7665444.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 @ Wed, 08 Dec 2021 18:05:41: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:05:41: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:05:44: 7000000 INFO @ Wed, 08 Dec 2021 18:05:46: 1000000 INFO @ Wed, 08 Dec 2021 18:05:49: 8000000 INFO @ Wed, 08 Dec 2021 18:05:51: 2000000 INFO @ Wed, 08 Dec 2021 18:05:54: 9000000 INFO @ Wed, 08 Dec 2021 18:05:56: 3000000 INFO @ Wed, 08 Dec 2021 18:05:59: 10000000 INFO @ Wed, 08 Dec 2021 18:06:01: 4000000 INFO @ Wed, 08 Dec 2021 18:06:03: 11000000 INFO @ Wed, 08 Dec 2021 18:06:06: 5000000 INFO @ Wed, 08 Dec 2021 18:06:08: 12000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 18:06:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7665444/SRX7665444.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7665444/SRX7665444.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7665444/SRX7665444.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7665444/SRX7665444.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 @ Wed, 08 Dec 2021 18:06:11: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:06:11: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:06:11: #1 tag size is determined as 36 bps INFO @ Wed, 08 Dec 2021 18:06:11: #1 tag size = 36 INFO @ Wed, 08 Dec 2021 18:06:11: #1 total tags in treatment: 12472972 INFO @ Wed, 08 Dec 2021 18:06:11: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:06:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 18:06:11: #1 tags after filtering in treatment: 12472972 INFO @ Wed, 08 Dec 2021 18:06:11: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 18:06:11: #1 finished! INFO @ Wed, 08 Dec 2021 18:06:11: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:06:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:06:11: 6000000 INFO @ Wed, 08 Dec 2021 18:06:12: #2 number of paired peaks: 716 WARNING @ Wed, 08 Dec 2021 18:06:12: Fewer paired peaks (716) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 716 pairs to build model! INFO @ Wed, 08 Dec 2021 18:06:12: start model_add_line... INFO @ Wed, 08 Dec 2021 18:06:12: start X-correlation... INFO @ Wed, 08 Dec 2021 18:06:12: end of X-cor INFO @ Wed, 08 Dec 2021 18:06:12: #2 finished! INFO @ Wed, 08 Dec 2021 18:06:12: #2 predicted fragment length is 104 bps INFO @ Wed, 08 Dec 2021 18:06:12: #2 alternative fragment length(s) may be 104 bps INFO @ Wed, 08 Dec 2021 18:06:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7665444/SRX7665444.05_model.r INFO @ Wed, 08 Dec 2021 18:06:12: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:06:12: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:06:16: 1000000 INFO @ Wed, 08 Dec 2021 18:06:16: 7000000 INFO @ Wed, 08 Dec 2021 18:06:21: 2000000 INFO @ Wed, 08 Dec 2021 18:06:21: 8000000 INFO @ Wed, 08 Dec 2021 18:06:26: 3000000 INFO @ Wed, 08 Dec 2021 18:06:26: 9000000 INFO @ Wed, 08 Dec 2021 18:06:31: 4000000 INFO @ Wed, 08 Dec 2021 18:06:31: 10000000 INFO @ Wed, 08 Dec 2021 18:06:35: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:06:36: 11000000 INFO @ Wed, 08 Dec 2021 18:06:36: 5000000 INFO @ Wed, 08 Dec 2021 18:06:41: 12000000 INFO @ Wed, 08 Dec 2021 18:06:41: 6000000 INFO @ Wed, 08 Dec 2021 18:06:44: #1 tag size is determined as 36 bps INFO @ Wed, 08 Dec 2021 18:06:44: #1 tag size = 36 INFO @ Wed, 08 Dec 2021 18:06:44: #1 total tags in treatment: 12472972 INFO @ Wed, 08 Dec 2021 18:06:44: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:06:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 18:06:44: #1 tags after filtering in treatment: 12472972 INFO @ Wed, 08 Dec 2021 18:06:44: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 18:06:44: #1 finished! INFO @ Wed, 08 Dec 2021 18:06:44: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:06:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:06:45: #2 number of paired peaks: 716 WARNING @ Wed, 08 Dec 2021 18:06:45: Fewer paired peaks (716) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 716 pairs to build model! INFO @ Wed, 08 Dec 2021 18:06:45: start model_add_line... INFO @ Wed, 08 Dec 2021 18:06:45: start X-correlation... INFO @ Wed, 08 Dec 2021 18:06:45: end of X-cor INFO @ Wed, 08 Dec 2021 18:06:45: #2 finished! INFO @ Wed, 08 Dec 2021 18:06:45: #2 predicted fragment length is 104 bps INFO @ Wed, 08 Dec 2021 18:06:45: #2 alternative fragment length(s) may be 104 bps INFO @ Wed, 08 Dec 2021 18:06:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7665444/SRX7665444.10_model.r INFO @ Wed, 08 Dec 2021 18:06:45: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:06:45: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:06:46: 7000000 INFO @ Wed, 08 Dec 2021 18:06:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7665444/SRX7665444.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:06:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7665444/SRX7665444.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:06:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7665444/SRX7665444.05_summits.bed INFO @ Wed, 08 Dec 2021 18:06:47: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6093 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:06:51: 8000000 INFO @ Wed, 08 Dec 2021 18:06:56: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:07:01: 10000000 INFO @ Wed, 08 Dec 2021 18:07:06: 11000000 INFO @ Wed, 08 Dec 2021 18:07:09: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:07:10: 12000000 INFO @ Wed, 08 Dec 2021 18:07:13: #1 tag size is determined as 36 bps INFO @ Wed, 08 Dec 2021 18:07:13: #1 tag size = 36 INFO @ Wed, 08 Dec 2021 18:07:13: #1 total tags in treatment: 12472972 INFO @ Wed, 08 Dec 2021 18:07:13: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:07:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 18:07:13: #1 tags after filtering in treatment: 12472972 INFO @ Wed, 08 Dec 2021 18:07:13: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 18:07:13: #1 finished! INFO @ Wed, 08 Dec 2021 18:07:13: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:07:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:07:14: #2 number of paired peaks: 716 WARNING @ Wed, 08 Dec 2021 18:07:14: Fewer paired peaks (716) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 716 pairs to build model! INFO @ Wed, 08 Dec 2021 18:07:14: start model_add_line... INFO @ Wed, 08 Dec 2021 18:07:14: start X-correlation... INFO @ Wed, 08 Dec 2021 18:07:14: end of X-cor INFO @ Wed, 08 Dec 2021 18:07:14: #2 finished! INFO @ Wed, 08 Dec 2021 18:07:14: #2 predicted fragment length is 104 bps INFO @ Wed, 08 Dec 2021 18:07:14: #2 alternative fragment length(s) may be 104 bps INFO @ Wed, 08 Dec 2021 18:07:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7665444/SRX7665444.20_model.r INFO @ Wed, 08 Dec 2021 18:07:14: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:07:14: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:07:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7665444/SRX7665444.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:07:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7665444/SRX7665444.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:07:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7665444/SRX7665444.10_summits.bed INFO @ Wed, 08 Dec 2021 18:07:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3621 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:07:37: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:07:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7665444/SRX7665444.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:07:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7665444/SRX7665444.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:07:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7665444/SRX7665444.20_summits.bed INFO @ Wed, 08 Dec 2021 18:07:49: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2008 records, 4 fields): 4 millis CompletedMACS2peakCalling