Job ID = 16434942 SRX = SRX10435528 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: 00:04:37 15770325 reads; of these: 15770325 (100.00%) were unpaired; of these: 2982111 (18.91%) aligned 0 times 10981301 (69.63%) aligned exactly 1 time 1806913 (11.46%) aligned >1 times 81.09% overall alignment rate Time searching: 00:04:37 Overall time: 00:04:37 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] 2034200 / 12788214 = 0.1591 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 10:25:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435528/SRX10435528.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435528/SRX10435528.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435528/SRX10435528.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10435528/SRX10435528.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 10:25:04: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:25:04: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:25:10: 1000000 INFO @ Tue, 02 Aug 2022 10:25:15: 2000000 INFO @ Tue, 02 Aug 2022 10:25:20: 3000000 INFO @ Tue, 02 Aug 2022 10:25:25: 4000000 INFO @ Tue, 02 Aug 2022 10:25:30: 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 10:25:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435528/SRX10435528.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435528/SRX10435528.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435528/SRX10435528.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10435528/SRX10435528.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 10:25:34: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:25:34: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:25:35: 6000000 INFO @ Tue, 02 Aug 2022 10:25:40: 1000000 INFO @ Tue, 02 Aug 2022 10:25:40: 7000000 INFO @ Tue, 02 Aug 2022 10:25:45: 2000000 INFO @ Tue, 02 Aug 2022 10:25:45: 8000000 INFO @ Tue, 02 Aug 2022 10:25:50: 9000000 INFO @ Tue, 02 Aug 2022 10:25:50: 3000000 INFO @ Tue, 02 Aug 2022 10:25:55: 10000000 INFO @ Tue, 02 Aug 2022 10:25:55: 4000000 INFO @ Tue, 02 Aug 2022 10:25:59: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:25:59: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:25:59: #1 total tags in treatment: 10754014 INFO @ Tue, 02 Aug 2022 10:25:59: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:25:59: #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 10:25:59: #1 tags after filtering in treatment: 10754014 INFO @ Tue, 02 Aug 2022 10:25:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:25:59: #1 finished! INFO @ Tue, 02 Aug 2022 10:25:59: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:25:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:26:00: #2 number of paired peaks: 927 WARNING @ Tue, 02 Aug 2022 10:26:00: Fewer paired peaks (927) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 927 pairs to build model! INFO @ Tue, 02 Aug 2022 10:26:00: start model_add_line... INFO @ Tue, 02 Aug 2022 10:26:00: start X-correlation... INFO @ Tue, 02 Aug 2022 10:26:00: end of X-cor INFO @ Tue, 02 Aug 2022 10:26:00: #2 finished! INFO @ Tue, 02 Aug 2022 10:26:00: #2 predicted fragment length is 175 bps INFO @ Tue, 02 Aug 2022 10:26:00: #2 alternative fragment length(s) may be 175 bps INFO @ Tue, 02 Aug 2022 10:26:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435528/SRX10435528.05_model.r INFO @ Tue, 02 Aug 2022 10:26:00: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:26:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:26:01: 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 10:26:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435528/SRX10435528.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435528/SRX10435528.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435528/SRX10435528.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10435528/SRX10435528.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 10:26:04: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:26:04: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:26:06: 6000000 INFO @ Tue, 02 Aug 2022 10:26:10: 1000000 INFO @ Tue, 02 Aug 2022 10:26:11: 7000000 INFO @ Tue, 02 Aug 2022 10:26:15: 2000000 INFO @ Tue, 02 Aug 2022 10:26:16: 8000000 INFO @ Tue, 02 Aug 2022 10:26:20: 3000000 INFO @ Tue, 02 Aug 2022 10:26:21: 9000000 INFO @ Tue, 02 Aug 2022 10:26:25: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:26:25: 4000000 INFO @ Tue, 02 Aug 2022 10:26:26: 10000000 INFO @ Tue, 02 Aug 2022 10:26:29: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:26:29: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:26:29: #1 total tags in treatment: 10754014 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 10:26:30: #1 tags after filtering in treatment: 10754014 INFO @ Tue, 02 Aug 2022 10:26:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:26:30: #1 finished! INFO @ Tue, 02 Aug 2022 10:26:30: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:26:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:26:30: 5000000 INFO @ Tue, 02 Aug 2022 10:26:30: #2 number of paired peaks: 927 WARNING @ Tue, 02 Aug 2022 10:26:30: Fewer paired peaks (927) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 927 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 10:26:31: end of X-cor INFO @ Tue, 02 Aug 2022 10:26:31: #2 finished! INFO @ Tue, 02 Aug 2022 10:26:31: #2 predicted fragment length is 175 bps INFO @ Tue, 02 Aug 2022 10:26:31: #2 alternative fragment length(s) may be 175 bps INFO @ Tue, 02 Aug 2022 10:26:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435528/SRX10435528.10_model.r INFO @ Tue, 02 Aug 2022 10:26:31: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:26:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:26:35: 6000000 INFO @ Tue, 02 Aug 2022 10:26:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435528/SRX10435528.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:26:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435528/SRX10435528.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:26:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435528/SRX10435528.05_summits.bed INFO @ Tue, 02 Aug 2022 10:26:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4015 records, 4 fields): 65 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:26:40: 7000000 INFO @ Tue, 02 Aug 2022 10:26:45: 8000000 INFO @ Tue, 02 Aug 2022 10:26:50: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:26:55: 10000000 INFO @ Tue, 02 Aug 2022 10:26:55: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:26:58: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:26:58: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:26:58: #1 total tags in treatment: 10754014 INFO @ Tue, 02 Aug 2022 10:26:58: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:26:58: #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 10:26:59: #1 tags after filtering in treatment: 10754014 INFO @ Tue, 02 Aug 2022 10:26:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:26:59: #1 finished! INFO @ Tue, 02 Aug 2022 10:26:59: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:26:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:26:59: #2 number of paired peaks: 927 WARNING @ Tue, 02 Aug 2022 10:26:59: Fewer paired peaks (927) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 927 pairs to build model! INFO @ Tue, 02 Aug 2022 10:26:59: start model_add_line... INFO @ Tue, 02 Aug 2022 10:26:59: start X-correlation... INFO @ Tue, 02 Aug 2022 10:26:59: end of X-cor INFO @ Tue, 02 Aug 2022 10:26:59: #2 finished! INFO @ Tue, 02 Aug 2022 10:26:59: #2 predicted fragment length is 175 bps INFO @ Tue, 02 Aug 2022 10:26:59: #2 alternative fragment length(s) may be 175 bps INFO @ Tue, 02 Aug 2022 10:26:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435528/SRX10435528.20_model.r INFO @ Tue, 02 Aug 2022 10:27:00: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:27:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:27:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435528/SRX10435528.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:27:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435528/SRX10435528.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:27:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435528/SRX10435528.10_summits.bed INFO @ Tue, 02 Aug 2022 10:27:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2515 records, 4 fields): 38 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:27:23: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:27:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435528/SRX10435528.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:27:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435528/SRX10435528.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:27:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435528/SRX10435528.20_summits.bed INFO @ Tue, 02 Aug 2022 10:27:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1437 records, 4 fields): 11 millis CompletedMACS2peakCalling