Job ID = 16434842 SRX = SRX10435516 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 17538842 spots for SRR14060948/SRR14060948.sra Written 17538842 spots for SRR14060948/SRR14060948.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434892 ("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: 00:05:43 17538842 reads; of these: 17538842 (100.00%) were unpaired; of these: 712500 (4.06%) aligned 0 times 14234750 (81.16%) aligned exactly 1 time 2591592 (14.78%) aligned >1 times 95.94% overall alignment rate Time searching: 00:05:43 Overall time: 00:05:43 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] 1861466 / 16826342 = 0.1106 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 10:11:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435516/SRX10435516.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435516/SRX10435516.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435516/SRX10435516.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435516/SRX10435516.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 10:11:39: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:11:39: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:11:45: 1000000 INFO @ Tue, 02 Aug 2022 10:11:51: 2000000 INFO @ Tue, 02 Aug 2022 10:11:57: 3000000 INFO @ Tue, 02 Aug 2022 10:12:02: 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 10:12:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435516/SRX10435516.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435516/SRX10435516.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435516/SRX10435516.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435516/SRX10435516.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 10:12:08: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:12:08: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:12:08: 5000000 INFO @ Tue, 02 Aug 2022 10:12:14: 6000000 INFO @ Tue, 02 Aug 2022 10:12:15: 1000000 INFO @ Tue, 02 Aug 2022 10:12:20: 7000000 INFO @ Tue, 02 Aug 2022 10:12:22: 2000000 INFO @ Tue, 02 Aug 2022 10:12:26: 8000000 INFO @ Tue, 02 Aug 2022 10:12:29: 3000000 INFO @ Tue, 02 Aug 2022 10:12:33: 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 10:12:36: 4000000 INFO @ Tue, 02 Aug 2022 10:12:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435516/SRX10435516.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435516/SRX10435516.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435516/SRX10435516.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435516/SRX10435516.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 10:12:38: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:12:38: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:12:39: 10000000 INFO @ Tue, 02 Aug 2022 10:12:44: 5000000 INFO @ Tue, 02 Aug 2022 10:12:45: 1000000 INFO @ Tue, 02 Aug 2022 10:12:45: 11000000 INFO @ Tue, 02 Aug 2022 10:12:51: 6000000 INFO @ Tue, 02 Aug 2022 10:12:52: 2000000 INFO @ Tue, 02 Aug 2022 10:12:52: 12000000 INFO @ Tue, 02 Aug 2022 10:12:58: 7000000 INFO @ Tue, 02 Aug 2022 10:12:59: 13000000 INFO @ Tue, 02 Aug 2022 10:12:59: 3000000 INFO @ Tue, 02 Aug 2022 10:13:05: 8000000 INFO @ Tue, 02 Aug 2022 10:13:05: 14000000 INFO @ Tue, 02 Aug 2022 10:13:06: 4000000 INFO @ Tue, 02 Aug 2022 10:13:11: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:13:11: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:13:11: #1 total tags in treatment: 14964876 INFO @ Tue, 02 Aug 2022 10:13:11: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:13:11: #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 10:13:11: 9000000 INFO @ Tue, 02 Aug 2022 10:13:11: #1 tags after filtering in treatment: 14964876 INFO @ Tue, 02 Aug 2022 10:13:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:13:11: #1 finished! INFO @ Tue, 02 Aug 2022 10:13:11: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:13:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:13:12: 5000000 INFO @ Tue, 02 Aug 2022 10:13:12: #2 number of paired peaks: 208 WARNING @ Tue, 02 Aug 2022 10:13:12: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Tue, 02 Aug 2022 10:13:12: start model_add_line... INFO @ Tue, 02 Aug 2022 10:13:12: start X-correlation... INFO @ Tue, 02 Aug 2022 10:13:13: end of X-cor INFO @ Tue, 02 Aug 2022 10:13:13: #2 finished! INFO @ Tue, 02 Aug 2022 10:13:13: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 10:13:13: #2 alternative fragment length(s) may be 3,74 bps INFO @ Tue, 02 Aug 2022 10:13:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435516/SRX10435516.05_model.r WARNING @ Tue, 02 Aug 2022 10:13:13: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:13:13: #2 You may need to consider one of the other alternative d(s): 3,74 WARNING @ Tue, 02 Aug 2022 10:13:13: #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 10:13:13: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:13:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:13:18: 10000000 INFO @ Tue, 02 Aug 2022 10:13:19: 6000000 INFO @ Tue, 02 Aug 2022 10:13:25: 11000000 INFO @ Tue, 02 Aug 2022 10:13:25: 7000000 INFO @ Tue, 02 Aug 2022 10:13:32: 8000000 INFO @ Tue, 02 Aug 2022 10:13:33: 12000000 INFO @ Tue, 02 Aug 2022 10:13:37: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:13:38: 9000000 INFO @ Tue, 02 Aug 2022 10:13:40: 13000000 INFO @ Tue, 02 Aug 2022 10:13:45: 10000000 INFO @ Tue, 02 Aug 2022 10:13:47: 14000000 INFO @ Tue, 02 Aug 2022 10:13:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435516/SRX10435516.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:13:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435516/SRX10435516.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:13:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435516/SRX10435516.05_summits.bed INFO @ Tue, 02 Aug 2022 10:13:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (734 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:13:51: 11000000 INFO @ Tue, 02 Aug 2022 10:13:53: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:13:53: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:13:53: #1 total tags in treatment: 14964876 INFO @ Tue, 02 Aug 2022 10:13:53: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:13:53: #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 10:13:54: #1 tags after filtering in treatment: 14964876 INFO @ Tue, 02 Aug 2022 10:13:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:13:54: #1 finished! INFO @ Tue, 02 Aug 2022 10:13:54: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:13:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:13:55: #2 number of paired peaks: 208 WARNING @ Tue, 02 Aug 2022 10:13:55: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Tue, 02 Aug 2022 10:13:55: start model_add_line... INFO @ Tue, 02 Aug 2022 10:13:55: start X-correlation... INFO @ Tue, 02 Aug 2022 10:13:55: end of X-cor INFO @ Tue, 02 Aug 2022 10:13:55: #2 finished! INFO @ Tue, 02 Aug 2022 10:13:55: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 10:13:55: #2 alternative fragment length(s) may be 3,74 bps INFO @ Tue, 02 Aug 2022 10:13:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435516/SRX10435516.10_model.r WARNING @ Tue, 02 Aug 2022 10:13:55: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:13:55: #2 You may need to consider one of the other alternative d(s): 3,74 WARNING @ Tue, 02 Aug 2022 10:13:55: #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 10:13:55: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:13:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:13:58: 12000000 INFO @ Tue, 02 Aug 2022 10:14:04: 13000000 INFO @ Tue, 02 Aug 2022 10:14:10: 14000000 INFO @ Tue, 02 Aug 2022 10:14:15: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:14:15: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:14:15: #1 total tags in treatment: 14964876 INFO @ Tue, 02 Aug 2022 10:14:15: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:14:15: #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 10:14:16: #1 tags after filtering in treatment: 14964876 INFO @ Tue, 02 Aug 2022 10:14:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:14:16: #1 finished! INFO @ Tue, 02 Aug 2022 10:14:16: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:14:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:14:17: #2 number of paired peaks: 208 WARNING @ Tue, 02 Aug 2022 10:14:17: Fewer paired peaks (208) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 208 pairs to build model! INFO @ Tue, 02 Aug 2022 10:14:17: start model_add_line... INFO @ Tue, 02 Aug 2022 10:14:17: start X-correlation... INFO @ Tue, 02 Aug 2022 10:14:17: end of X-cor INFO @ Tue, 02 Aug 2022 10:14:17: #2 finished! INFO @ Tue, 02 Aug 2022 10:14:17: #2 predicted fragment length is 74 bps INFO @ Tue, 02 Aug 2022 10:14:17: #2 alternative fragment length(s) may be 3,74 bps INFO @ Tue, 02 Aug 2022 10:14:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435516/SRX10435516.20_model.r WARNING @ Tue, 02 Aug 2022 10:14:17: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:14:17: #2 You may need to consider one of the other alternative d(s): 3,74 WARNING @ Tue, 02 Aug 2022 10:14:17: #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 10:14:17: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:14:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:14:20: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:14:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435516/SRX10435516.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:14:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435516/SRX10435516.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:14:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435516/SRX10435516.10_summits.bed INFO @ Tue, 02 Aug 2022 10:14:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (402 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:14:42: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:14:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435516/SRX10435516.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:14:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435516/SRX10435516.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:14:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435516/SRX10435516.20_summits.bed INFO @ Tue, 02 Aug 2022 10:14:54: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (222 records, 4 fields): 12 millis CompletedMACS2peakCalling BigWig に変換しました。