Job ID = 14160369 SRX = SRX9567185 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 29335074 spots for SRR13125160/SRR13125160.sra Written 29335074 spots for SRR13125160/SRR13125160.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160695 ("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: 01:22:22 29335074 reads; of these: 29335074 (100.00%) were paired; of these: 8318897 (28.36%) aligned concordantly 0 times 18139251 (61.83%) aligned concordantly exactly 1 time 2876926 (9.81%) aligned concordantly >1 times ---- 8318897 pairs aligned concordantly 0 times; of these: 5833011 (70.12%) aligned discordantly 1 time ---- 2485886 pairs aligned 0 times concordantly or discordantly; of these: 4971772 mates make up the pairs; of these: 2270653 (45.67%) aligned 0 times 1330811 (26.77%) aligned exactly 1 time 1370308 (27.56%) aligned >1 times 96.13% overall alignment rate Time searching: 01:22:22 Overall time: 01:22:22 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 44 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 20452182 / 26821626 = 0.7625 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 @ Thu, 09 Dec 2021 03:39:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567185/SRX9567185.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567185/SRX9567185.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567185/SRX9567185.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567185/SRX9567185.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 @ Thu, 09 Dec 2021 03:39:03: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:39:03: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:39:22: 1000000 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 @ Thu, 09 Dec 2021 03:39:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567185/SRX9567185.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567185/SRX9567185.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567185/SRX9567185.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567185/SRX9567185.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 @ Thu, 09 Dec 2021 03:39:32: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:39:32: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:39:42: 2000000 INFO @ Thu, 09 Dec 2021 03:39:47: 1000000 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 @ Thu, 09 Dec 2021 03:40:00: 3000000 INFO @ Thu, 09 Dec 2021 03:40:02: 2000000 INFO @ Thu, 09 Dec 2021 03:40:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567185/SRX9567185.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567185/SRX9567185.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567185/SRX9567185.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567185/SRX9567185.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 @ Thu, 09 Dec 2021 03:40:02: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:40:02: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:40:17: 3000000 INFO @ Thu, 09 Dec 2021 03:40:19: 4000000 INFO @ Thu, 09 Dec 2021 03:40:19: 1000000 INFO @ Thu, 09 Dec 2021 03:40:32: 4000000 INFO @ Thu, 09 Dec 2021 03:40:36: 2000000 INFO @ Thu, 09 Dec 2021 03:40:37: 5000000 INFO @ Thu, 09 Dec 2021 03:40:47: 5000000 INFO @ Thu, 09 Dec 2021 03:40:51: 3000000 INFO @ Thu, 09 Dec 2021 03:40:57: 6000000 INFO @ Thu, 09 Dec 2021 03:41:02: 6000000 INFO @ Thu, 09 Dec 2021 03:41:05: 4000000 INFO @ Thu, 09 Dec 2021 03:41:17: 7000000 INFO @ Thu, 09 Dec 2021 03:41:19: 7000000 INFO @ Thu, 09 Dec 2021 03:41:21: 5000000 INFO @ Thu, 09 Dec 2021 03:41:34: 8000000 INFO @ Thu, 09 Dec 2021 03:41:35: 6000000 INFO @ Thu, 09 Dec 2021 03:41:37: 8000000 INFO @ Thu, 09 Dec 2021 03:41:49: 9000000 INFO @ Thu, 09 Dec 2021 03:41:50: 7000000 INFO @ Thu, 09 Dec 2021 03:41:57: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:42:03: 10000000 INFO @ Thu, 09 Dec 2021 03:42:04: 8000000 INFO @ Thu, 09 Dec 2021 03:42:16: 10000000 INFO @ Thu, 09 Dec 2021 03:42:18: 11000000 INFO @ Thu, 09 Dec 2021 03:42:18: 9000000 INFO @ Thu, 09 Dec 2021 03:42:32: 10000000 INFO @ Thu, 09 Dec 2021 03:42:33: 12000000 INFO @ Thu, 09 Dec 2021 03:42:36: 11000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:42:47: 11000000 INFO @ Thu, 09 Dec 2021 03:42:47: 13000000 INFO @ Thu, 09 Dec 2021 03:42:55: 12000000 INFO @ Thu, 09 Dec 2021 03:43:01: 12000000 INFO @ Thu, 09 Dec 2021 03:43:02: 14000000 INFO @ Thu, 09 Dec 2021 03:43:15: 13000000 INFO @ Thu, 09 Dec 2021 03:43:15: 13000000 INFO @ Thu, 09 Dec 2021 03:43:17: 15000000 INFO @ Thu, 09 Dec 2021 03:43:24: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:43:24: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:43:24: #1 total tags in treatment: 5079194 INFO @ Thu, 09 Dec 2021 03:43:24: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:43:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:43:24: #1 tags after filtering in treatment: 4561783 INFO @ Thu, 09 Dec 2021 03:43:24: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 09 Dec 2021 03:43:24: #1 finished! INFO @ Thu, 09 Dec 2021 03:43:24: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:43:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:43:25: #2 number of paired peaks: 684 WARNING @ Thu, 09 Dec 2021 03:43:25: Fewer paired peaks (684) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 684 pairs to build model! INFO @ Thu, 09 Dec 2021 03:43:25: start model_add_line... INFO @ Thu, 09 Dec 2021 03:43:25: start X-correlation... INFO @ Thu, 09 Dec 2021 03:43:25: end of X-cor INFO @ Thu, 09 Dec 2021 03:43:25: #2 finished! INFO @ Thu, 09 Dec 2021 03:43:25: #2 predicted fragment length is 227 bps INFO @ Thu, 09 Dec 2021 03:43:25: #2 alternative fragment length(s) may be 227 bps INFO @ Thu, 09 Dec 2021 03:43:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567185/SRX9567185.10_model.r WARNING @ Thu, 09 Dec 2021 03:43:25: #2 Since the d (227) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:43:25: #2 You may need to consider one of the other alternative d(s): 227 WARNING @ Thu, 09 Dec 2021 03:43:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:43:25: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:43:25: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:43:29: 14000000 INFO @ Thu, 09 Dec 2021 03:43:34: 14000000 INFO @ Thu, 09 Dec 2021 03:43:41: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:43:43: 15000000 INFO @ Thu, 09 Dec 2021 03:43:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567185/SRX9567185.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:43:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567185/SRX9567185.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:43:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567185/SRX9567185.10_summits.bed INFO @ Thu, 09 Dec 2021 03:43:49: Done! INFO @ Thu, 09 Dec 2021 03:43:49: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:43:49: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:43:49: #1 total tags in treatment: 5079194 INFO @ Thu, 09 Dec 2021 03:43:49: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:43:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (7 chroms): 1 millis INFO @ Thu, 09 Dec 2021 03:43:49: #1 tags after filtering in treatment: 4561783 INFO @ Thu, 09 Dec 2021 03:43:49: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 09 Dec 2021 03:43:49: #1 finished! INFO @ Thu, 09 Dec 2021 03:43:49: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:43:49: #2 looking for paired plus/minus strand peaks... pass2 - checking and writing primary data (401 records, 4 fields): 199 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:43:50: #2 number of paired peaks: 684 WARNING @ Thu, 09 Dec 2021 03:43:50: Fewer paired peaks (684) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 684 pairs to build model! INFO @ Thu, 09 Dec 2021 03:43:50: start model_add_line... INFO @ Thu, 09 Dec 2021 03:43:50: start X-correlation... INFO @ Thu, 09 Dec 2021 03:43:50: end of X-cor INFO @ Thu, 09 Dec 2021 03:43:50: #2 finished! INFO @ Thu, 09 Dec 2021 03:43:50: #2 predicted fragment length is 227 bps INFO @ Thu, 09 Dec 2021 03:43:50: #2 alternative fragment length(s) may be 227 bps INFO @ Thu, 09 Dec 2021 03:43:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567185/SRX9567185.20_model.r WARNING @ Thu, 09 Dec 2021 03:43:50: #2 Since the d (227) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:43:50: #2 You may need to consider one of the other alternative d(s): 227 WARNING @ Thu, 09 Dec 2021 03:43:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:43:50: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:43:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:43:53: 15000000 INFO @ Thu, 09 Dec 2021 03:44:01: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:44:01: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:44:01: #1 total tags in treatment: 5079194 INFO @ Thu, 09 Dec 2021 03:44:01: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:44:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:44:01: #1 tags after filtering in treatment: 4561783 INFO @ Thu, 09 Dec 2021 03:44:01: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 09 Dec 2021 03:44:01: #1 finished! INFO @ Thu, 09 Dec 2021 03:44:01: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:44:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:44:02: #2 number of paired peaks: 684 WARNING @ Thu, 09 Dec 2021 03:44:02: Fewer paired peaks (684) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 684 pairs to build model! INFO @ Thu, 09 Dec 2021 03:44:02: start model_add_line... INFO @ Thu, 09 Dec 2021 03:44:02: start X-correlation... INFO @ Thu, 09 Dec 2021 03:44:02: end of X-cor INFO @ Thu, 09 Dec 2021 03:44:02: #2 finished! INFO @ Thu, 09 Dec 2021 03:44:02: #2 predicted fragment length is 227 bps INFO @ Thu, 09 Dec 2021 03:44:02: #2 alternative fragment length(s) may be 227 bps INFO @ Thu, 09 Dec 2021 03:44:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567185/SRX9567185.05_model.r WARNING @ Thu, 09 Dec 2021 03:44:02: #2 Since the d (227) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:44:02: #2 You may need to consider one of the other alternative d(s): 227 WARNING @ Thu, 09 Dec 2021 03:44:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:44:02: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:44:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:44:06: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:44:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567185/SRX9567185.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:44:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567185/SRX9567185.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:44:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567185/SRX9567185.20_summits.bed INFO @ Thu, 09 Dec 2021 03:44:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (290 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:44:18: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:44:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567185/SRX9567185.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:44:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567185/SRX9567185.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:44:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567185/SRX9567185.05_summits.bed INFO @ Thu, 09 Dec 2021 03:44:26: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (602 records, 4 fields): 4 millis CompletedMACS2peakCalling