Job ID = 16434976 SRX = SRX10435541 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 12325667 spots for SRR14060957/SRR14060957.sra Written 12325667 spots for SRR14060957/SRR14060957.sra fastq に変換しました。 bowtie でマッピング中... Your job 16435020 ("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: 00:04:04 12325667 reads; of these: 12325667 (100.00%) were unpaired; of these: 614303 (4.98%) aligned 0 times 9702935 (78.72%) aligned exactly 1 time 2008429 (16.29%) aligned >1 times 95.02% overall alignment rate Time searching: 00:04:04 Overall time: 00:04:04 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] 1033544 / 11711364 = 0.0883 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 10:31:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435541/SRX10435541.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435541/SRX10435541.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435541/SRX10435541.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435541/SRX10435541.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 10:31:37: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:31:37: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:31:43: 1000000 INFO @ Tue, 02 Aug 2022 10:31:48: 2000000 INFO @ Tue, 02 Aug 2022 10:31:54: 3000000 INFO @ Tue, 02 Aug 2022 10:31:59: 4000000 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 10:32:05: 5000000 INFO @ Tue, 02 Aug 2022 10:32:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435541/SRX10435541.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435541/SRX10435541.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435541/SRX10435541.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435541/SRX10435541.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 10:32:07: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:32:07: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:32:11: 6000000 INFO @ Tue, 02 Aug 2022 10:32:14: 1000000 INFO @ Tue, 02 Aug 2022 10:32:17: 7000000 INFO @ Tue, 02 Aug 2022 10:32:22: 2000000 INFO @ Tue, 02 Aug 2022 10:32:24: 8000000 INFO @ Tue, 02 Aug 2022 10:32:28: 3000000 INFO @ Tue, 02 Aug 2022 10:32:30: 9000000 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 10:32:35: 4000000 INFO @ Tue, 02 Aug 2022 10:32:36: 10000000 INFO @ Tue, 02 Aug 2022 10:32:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435541/SRX10435541.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435541/SRX10435541.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435541/SRX10435541.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435541/SRX10435541.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 10:32:37: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:32:37: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:32:41: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:32:41: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:32:41: #1 total tags in treatment: 10677820 INFO @ Tue, 02 Aug 2022 10:32:41: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:32:41: #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 10:32:41: #1 tags after filtering in treatment: 10677820 INFO @ Tue, 02 Aug 2022 10:32:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:32:41: #1 finished! INFO @ Tue, 02 Aug 2022 10:32:41: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:32:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:32:42: #2 number of paired peaks: 319 WARNING @ Tue, 02 Aug 2022 10:32:42: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Tue, 02 Aug 2022 10:32:42: start model_add_line... INFO @ Tue, 02 Aug 2022 10:32:42: start X-correlation... INFO @ Tue, 02 Aug 2022 10:32:42: end of X-cor INFO @ Tue, 02 Aug 2022 10:32:42: #2 finished! INFO @ Tue, 02 Aug 2022 10:32:42: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 10:32:42: #2 alternative fragment length(s) may be 4,72 bps INFO @ Tue, 02 Aug 2022 10:32:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435541/SRX10435541.05_model.r WARNING @ Tue, 02 Aug 2022 10:32:42: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:32:42: #2 You may need to consider one of the other alternative d(s): 4,72 WARNING @ Tue, 02 Aug 2022 10:32:42: #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 10:32:42: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:32:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:32:42: 5000000 INFO @ Tue, 02 Aug 2022 10:32:44: 1000000 INFO @ Tue, 02 Aug 2022 10:32:49: 6000000 INFO @ Tue, 02 Aug 2022 10:32:50: 2000000 INFO @ Tue, 02 Aug 2022 10:32:55: 7000000 INFO @ Tue, 02 Aug 2022 10:32:57: 3000000 INFO @ Tue, 02 Aug 2022 10:33:02: 8000000 INFO @ Tue, 02 Aug 2022 10:33:04: 4000000 INFO @ Tue, 02 Aug 2022 10:33:04: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:33:09: 9000000 INFO @ Tue, 02 Aug 2022 10:33:11: 5000000 INFO @ Tue, 02 Aug 2022 10:33:15: 10000000 INFO @ Tue, 02 Aug 2022 10:33:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435541/SRX10435541.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:33:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435541/SRX10435541.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:33:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435541/SRX10435541.05_summits.bed INFO @ Tue, 02 Aug 2022 10:33:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (573 records, 4 fields): 40 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:33:17: 6000000 INFO @ Tue, 02 Aug 2022 10:33:19: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:33:19: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:33:19: #1 total tags in treatment: 10677820 INFO @ Tue, 02 Aug 2022 10:33:19: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:33:19: #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 10:33:19: #1 tags after filtering in treatment: 10677820 INFO @ Tue, 02 Aug 2022 10:33:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:33:19: #1 finished! INFO @ Tue, 02 Aug 2022 10:33:19: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:33:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:33:20: #2 number of paired peaks: 319 WARNING @ Tue, 02 Aug 2022 10:33:20: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Tue, 02 Aug 2022 10:33:20: start model_add_line... INFO @ Tue, 02 Aug 2022 10:33:20: start X-correlation... INFO @ Tue, 02 Aug 2022 10:33:20: end of X-cor INFO @ Tue, 02 Aug 2022 10:33:20: #2 finished! INFO @ Tue, 02 Aug 2022 10:33:20: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 10:33:20: #2 alternative fragment length(s) may be 4,72 bps INFO @ Tue, 02 Aug 2022 10:33:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435541/SRX10435541.10_model.r WARNING @ Tue, 02 Aug 2022 10:33:20: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:33:20: #2 You may need to consider one of the other alternative d(s): 4,72 WARNING @ Tue, 02 Aug 2022 10:33:20: #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 10:33:20: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:33:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:33:23: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:33:29: 8000000 INFO @ Tue, 02 Aug 2022 10:33:35: 9000000 INFO @ Tue, 02 Aug 2022 10:33:41: 10000000 INFO @ Tue, 02 Aug 2022 10:33:42: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:33:44: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:33:44: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:33:44: #1 total tags in treatment: 10677820 INFO @ Tue, 02 Aug 2022 10:33:44: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:33:44: #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 10:33:45: #1 tags after filtering in treatment: 10677820 INFO @ Tue, 02 Aug 2022 10:33:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:33:45: #1 finished! INFO @ Tue, 02 Aug 2022 10:33:45: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:33:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:33:45: #2 number of paired peaks: 319 WARNING @ Tue, 02 Aug 2022 10:33:45: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Tue, 02 Aug 2022 10:33:45: start model_add_line... INFO @ Tue, 02 Aug 2022 10:33:45: start X-correlation... INFO @ Tue, 02 Aug 2022 10:33:45: end of X-cor INFO @ Tue, 02 Aug 2022 10:33:45: #2 finished! INFO @ Tue, 02 Aug 2022 10:33:45: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 10:33:45: #2 alternative fragment length(s) may be 4,72 bps INFO @ Tue, 02 Aug 2022 10:33:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435541/SRX10435541.20_model.r WARNING @ Tue, 02 Aug 2022 10:33:45: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:33:45: #2 You may need to consider one of the other alternative d(s): 4,72 WARNING @ Tue, 02 Aug 2022 10:33:45: #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 10:33:45: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:33:45: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:33:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435541/SRX10435541.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:33:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435541/SRX10435541.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:33:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435541/SRX10435541.10_summits.bed INFO @ Tue, 02 Aug 2022 10:33:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (393 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:34:06: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:34:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435541/SRX10435541.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:34:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435541/SRX10435541.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:34:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435541/SRX10435541.20_summits.bed INFO @ Tue, 02 Aug 2022 10:34:16: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (220 records, 4 fields): 12 millis CompletedMACS2peakCalling