Job ID = 16435003 SRX = SRX10435542 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 16476072 spots for SRR14060958/SRR14060958.sra Written 16476072 spots for SRR14060958/SRR14060958.sra fastq に変換しました。 bowtie でマッピング中... Your job 16435140 ("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: 00:05:34 16476072 reads; of these: 16476072 (100.00%) were unpaired; of these: 308363 (1.87%) aligned 0 times 13330541 (80.91%) aligned exactly 1 time 2837168 (17.22%) aligned >1 times 98.13% overall alignment rate Time searching: 00:05:34 Overall time: 00:05:34 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] 1739868 / 16167709 = 0.1076 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 10:38:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435542/SRX10435542.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435542/SRX10435542.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435542/SRX10435542.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435542/SRX10435542.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 10:38:31: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:38:31: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:38:39: 1000000 INFO @ Tue, 02 Aug 2022 10:38:46: 2000000 INFO @ Tue, 02 Aug 2022 10:38:53: 3000000 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 10:39:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435542/SRX10435542.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435542/SRX10435542.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435542/SRX10435542.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435542/SRX10435542.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 10:39:00: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:39:00: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:39:00: 4000000 INFO @ Tue, 02 Aug 2022 10:39:09: 5000000 INFO @ Tue, 02 Aug 2022 10:39:09: 1000000 INFO @ Tue, 02 Aug 2022 10:39:17: 6000000 INFO @ Tue, 02 Aug 2022 10:39:17: 2000000 INFO @ Tue, 02 Aug 2022 10:39:24: 7000000 INFO @ Tue, 02 Aug 2022 10:39:24: 3000000 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 10:39:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435542/SRX10435542.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435542/SRX10435542.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435542/SRX10435542.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435542/SRX10435542.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 10:39:30: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:39:30: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:39:32: 4000000 INFO @ Tue, 02 Aug 2022 10:39:32: 8000000 INFO @ Tue, 02 Aug 2022 10:39:38: 1000000 INFO @ Tue, 02 Aug 2022 10:39:40: 5000000 INFO @ Tue, 02 Aug 2022 10:39:40: 9000000 INFO @ Tue, 02 Aug 2022 10:39:46: 2000000 INFO @ Tue, 02 Aug 2022 10:39:47: 6000000 INFO @ Tue, 02 Aug 2022 10:39:48: 10000000 INFO @ Tue, 02 Aug 2022 10:39:54: 3000000 INFO @ Tue, 02 Aug 2022 10:39:55: 7000000 INFO @ Tue, 02 Aug 2022 10:39:57: 11000000 INFO @ Tue, 02 Aug 2022 10:40:02: 4000000 INFO @ Tue, 02 Aug 2022 10:40:04: 8000000 INFO @ Tue, 02 Aug 2022 10:40:05: 12000000 INFO @ Tue, 02 Aug 2022 10:40:09: 5000000 INFO @ Tue, 02 Aug 2022 10:40:12: 9000000 INFO @ Tue, 02 Aug 2022 10:40:13: 13000000 INFO @ Tue, 02 Aug 2022 10:40:17: 6000000 INFO @ Tue, 02 Aug 2022 10:40:20: 10000000 INFO @ Tue, 02 Aug 2022 10:40:22: 14000000 INFO @ Tue, 02 Aug 2022 10:40:25: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:40:25: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:40:25: #1 total tags in treatment: 14427841 INFO @ Tue, 02 Aug 2022 10:40:25: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:40:25: #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 10:40:25: 7000000 INFO @ Tue, 02 Aug 2022 10:40:26: #1 tags after filtering in treatment: 14427841 INFO @ Tue, 02 Aug 2022 10:40:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:40:26: #1 finished! INFO @ Tue, 02 Aug 2022 10:40:26: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:40:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:40:27: #2 number of paired peaks: 280 WARNING @ Tue, 02 Aug 2022 10:40:27: Fewer paired peaks (280) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 280 pairs to build model! INFO @ Tue, 02 Aug 2022 10:40:27: start model_add_line... INFO @ Tue, 02 Aug 2022 10:40:27: start X-correlation... INFO @ Tue, 02 Aug 2022 10:40:27: end of X-cor INFO @ Tue, 02 Aug 2022 10:40:27: #2 finished! INFO @ Tue, 02 Aug 2022 10:40:27: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 10:40:27: #2 alternative fragment length(s) may be 4,71 bps INFO @ Tue, 02 Aug 2022 10:40:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435542/SRX10435542.05_model.r WARNING @ Tue, 02 Aug 2022 10:40:27: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:40:27: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Tue, 02 Aug 2022 10:40:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:40:27: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:40:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:40:28: 11000000 INFO @ Tue, 02 Aug 2022 10:40:33: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:40:36: 12000000 INFO @ Tue, 02 Aug 2022 10:40:41: 9000000 INFO @ Tue, 02 Aug 2022 10:40:44: 13000000 INFO @ Tue, 02 Aug 2022 10:40:49: 10000000 INFO @ Tue, 02 Aug 2022 10:40:51: 14000000 INFO @ Tue, 02 Aug 2022 10:40:53: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:40:55: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:40:55: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:40:55: #1 total tags in treatment: 14427841 INFO @ Tue, 02 Aug 2022 10:40:55: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:40:55: #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 10:40:55: #1 tags after filtering in treatment: 14427841 INFO @ Tue, 02 Aug 2022 10:40:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:40:55: #1 finished! INFO @ Tue, 02 Aug 2022 10:40:55: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:40:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:40:56: #2 number of paired peaks: 280 WARNING @ Tue, 02 Aug 2022 10:40:56: Fewer paired peaks (280) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 280 pairs to build model! INFO @ Tue, 02 Aug 2022 10:40:56: start model_add_line... INFO @ Tue, 02 Aug 2022 10:40:56: start X-correlation... INFO @ Tue, 02 Aug 2022 10:40:56: end of X-cor INFO @ Tue, 02 Aug 2022 10:40:56: #2 finished! INFO @ Tue, 02 Aug 2022 10:40:56: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 10:40:56: #2 alternative fragment length(s) may be 4,71 bps INFO @ Tue, 02 Aug 2022 10:40:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435542/SRX10435542.10_model.r WARNING @ Tue, 02 Aug 2022 10:40:56: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:40:56: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Tue, 02 Aug 2022 10:40:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:40:56: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:40:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:40:57: 11000000 INFO @ Tue, 02 Aug 2022 10:41:04: 12000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:41:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435542/SRX10435542.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:41:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435542/SRX10435542.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:41:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435542/SRX10435542.05_summits.bed INFO @ Tue, 02 Aug 2022 10:41:06: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (948 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:41:11: 13000000 INFO @ Tue, 02 Aug 2022 10:41:18: 14000000 INFO @ Tue, 02 Aug 2022 10:41:20: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:41:20: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:41:20: #1 total tags in treatment: 14427841 INFO @ Tue, 02 Aug 2022 10:41:20: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:41:20: #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 10:41:21: #1 tags after filtering in treatment: 14427841 INFO @ Tue, 02 Aug 2022 10:41:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:41:21: #1 finished! INFO @ Tue, 02 Aug 2022 10:41:21: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:41:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:41:22: #2 number of paired peaks: 280 WARNING @ Tue, 02 Aug 2022 10:41:22: Fewer paired peaks (280) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 280 pairs to build model! INFO @ Tue, 02 Aug 2022 10:41:22: start model_add_line... INFO @ Tue, 02 Aug 2022 10:41:22: start X-correlation... INFO @ Tue, 02 Aug 2022 10:41:22: end of X-cor INFO @ Tue, 02 Aug 2022 10:41:22: #2 finished! INFO @ Tue, 02 Aug 2022 10:41:22: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 10:41:22: #2 alternative fragment length(s) may be 4,71 bps INFO @ Tue, 02 Aug 2022 10:41:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435542/SRX10435542.20_model.r WARNING @ Tue, 02 Aug 2022 10:41:22: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:41:22: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Tue, 02 Aug 2022 10:41:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:41:22: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:41:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:41:22: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:41:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435542/SRX10435542.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:41:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435542/SRX10435542.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:41:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435542/SRX10435542.10_summits.bed INFO @ Tue, 02 Aug 2022 10:41:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (488 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:41:49: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:42:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435542/SRX10435542.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:42:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435542/SRX10435542.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:42:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435542/SRX10435542.20_summits.bed INFO @ Tue, 02 Aug 2022 10:42:02: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (237 records, 4 fields): 132 millis CompletedMACS2peakCalling