Job ID = 14160557 SRX = SRX9567166 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED 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: 01:20:11 19598085 reads; of these: 19598085 (100.00%) were paired; of these: 8644740 (44.11%) aligned concordantly 0 times 6316712 (32.23%) aligned concordantly exactly 1 time 4636633 (23.66%) aligned concordantly >1 times ---- 8644740 pairs aligned concordantly 0 times; of these: 4435021 (51.30%) aligned discordantly 1 time ---- 4209719 pairs aligned 0 times concordantly or discordantly; of these: 8419438 mates make up the pairs; of these: 6238247 (74.09%) aligned 0 times 972645 (11.55%) aligned exactly 1 time 1208546 (14.35%) aligned >1 times 84.08% overall alignment rate Time searching: 01:20:11 Overall time: 01:20:11 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 24 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] 12415368 / 15368453 = 0.8078 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 04:44:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9567166/SRX9567166.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9567166/SRX9567166.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9567166/SRX9567166.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9567166/SRX9567166.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 04:44:24: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:44:24: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:44:38: 1000000 INFO @ Thu, 09 Dec 2021 04:44:50: 2000000 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 04:44:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9567166/SRX9567166.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9567166/SRX9567166.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9567166/SRX9567166.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9567166/SRX9567166.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 04:44:54: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:44:54: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:45:02: 3000000 INFO @ Thu, 09 Dec 2021 04:45:07: 1000000 INFO @ Thu, 09 Dec 2021 04:45:15: 4000000 INFO @ Thu, 09 Dec 2021 04:45:19: 2000000 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 04:45:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9567166/SRX9567166.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9567166/SRX9567166.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9567166/SRX9567166.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9567166/SRX9567166.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 04:45:24: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:45:24: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:45:28: 5000000 INFO @ Thu, 09 Dec 2021 04:45:32: 3000000 INFO @ Thu, 09 Dec 2021 04:45:39: 1000000 INFO @ Thu, 09 Dec 2021 04:45:42: 6000000 INFO @ Thu, 09 Dec 2021 04:45:44: 4000000 INFO @ Thu, 09 Dec 2021 04:45:53: 2000000 INFO @ Thu, 09 Dec 2021 04:45:56: 7000000 INFO @ Thu, 09 Dec 2021 04:45:56: 5000000 INFO @ Thu, 09 Dec 2021 04:46:07: 3000000 INFO @ Thu, 09 Dec 2021 04:46:08: 6000000 INFO @ Thu, 09 Dec 2021 04:46:09: 8000000 INFO @ Thu, 09 Dec 2021 04:46:11: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 04:46:11: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 04:46:11: #1 total tags in treatment: 2196657 INFO @ Thu, 09 Dec 2021 04:46:11: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:46:11: #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 04:46:11: #1 tags after filtering in treatment: 1440159 INFO @ Thu, 09 Dec 2021 04:46:11: #1 Redundant rate of treatment: 0.34 INFO @ Thu, 09 Dec 2021 04:46:11: #1 finished! INFO @ Thu, 09 Dec 2021 04:46:11: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:46:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:46:11: #2 number of paired peaks: 1020 INFO @ Thu, 09 Dec 2021 04:46:11: start model_add_line... INFO @ Thu, 09 Dec 2021 04:46:11: start X-correlation... INFO @ Thu, 09 Dec 2021 04:46:11: end of X-cor INFO @ Thu, 09 Dec 2021 04:46:11: #2 finished! INFO @ Thu, 09 Dec 2021 04:46:11: #2 predicted fragment length is 291 bps INFO @ Thu, 09 Dec 2021 04:46:11: #2 alternative fragment length(s) may be 291 bps INFO @ Thu, 09 Dec 2021 04:46:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9567166/SRX9567166.05_model.r WARNING @ Thu, 09 Dec 2021 04:46:11: #2 Since the d (291) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:46:11: #2 You may need to consider one of the other alternative d(s): 291 WARNING @ Thu, 09 Dec 2021 04:46:11: #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 04:46:11: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:46:11: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:46:18: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:46:20: 7000000 INFO @ Thu, 09 Dec 2021 04:46:21: 4000000 INFO @ Thu, 09 Dec 2021 04:46:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9567166/SRX9567166.05_peaks.xls INFO @ Thu, 09 Dec 2021 04:46:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9567166/SRX9567166.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:46:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9567166/SRX9567166.05_summits.bed INFO @ Thu, 09 Dec 2021 04:46:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (729 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 04:46:32: 8000000 INFO @ Thu, 09 Dec 2021 04:46:33: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 04:46:33: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 04:46:33: #1 total tags in treatment: 2196657 INFO @ Thu, 09 Dec 2021 04:46:33: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:46:33: #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 04:46:33: #1 tags after filtering in treatment: 1440159 INFO @ Thu, 09 Dec 2021 04:46:33: #1 Redundant rate of treatment: 0.34 INFO @ Thu, 09 Dec 2021 04:46:33: #1 finished! INFO @ Thu, 09 Dec 2021 04:46:33: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:46:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:46:33: #2 number of paired peaks: 1020 INFO @ Thu, 09 Dec 2021 04:46:33: start model_add_line... INFO @ Thu, 09 Dec 2021 04:46:33: start X-correlation... INFO @ Thu, 09 Dec 2021 04:46:33: end of X-cor INFO @ Thu, 09 Dec 2021 04:46:33: #2 finished! INFO @ Thu, 09 Dec 2021 04:46:33: #2 predicted fragment length is 291 bps INFO @ Thu, 09 Dec 2021 04:46:33: #2 alternative fragment length(s) may be 291 bps INFO @ Thu, 09 Dec 2021 04:46:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9567166/SRX9567166.10_model.r WARNING @ Thu, 09 Dec 2021 04:46:33: #2 Since the d (291) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:46:33: #2 You may need to consider one of the other alternative d(s): 291 WARNING @ Thu, 09 Dec 2021 04:46:33: #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 04:46:33: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:46:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:46:34: 5000000 INFO @ Thu, 09 Dec 2021 04:46:40: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 04:46:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9567166/SRX9567166.10_peaks.xls INFO @ Thu, 09 Dec 2021 04:46:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9567166/SRX9567166.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:46:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9567166/SRX9567166.10_summits.bed INFO @ Thu, 09 Dec 2021 04:46:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (529 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:46:47: 6000000 INFO @ Thu, 09 Dec 2021 04:47:00: 7000000 INFO @ Thu, 09 Dec 2021 04:47:12: 8000000 INFO @ Thu, 09 Dec 2021 04:47:13: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 04:47:13: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 04:47:13: #1 total tags in treatment: 2196657 INFO @ Thu, 09 Dec 2021 04:47:13: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:47:13: #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 04:47:13: #1 tags after filtering in treatment: 1440159 INFO @ Thu, 09 Dec 2021 04:47:13: #1 Redundant rate of treatment: 0.34 INFO @ Thu, 09 Dec 2021 04:47:13: #1 finished! INFO @ Thu, 09 Dec 2021 04:47:13: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:47:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:47:14: #2 number of paired peaks: 1020 INFO @ Thu, 09 Dec 2021 04:47:14: start model_add_line... INFO @ Thu, 09 Dec 2021 04:47:14: start X-correlation... INFO @ Thu, 09 Dec 2021 04:47:14: end of X-cor INFO @ Thu, 09 Dec 2021 04:47:14: #2 finished! INFO @ Thu, 09 Dec 2021 04:47:14: #2 predicted fragment length is 291 bps INFO @ Thu, 09 Dec 2021 04:47:14: #2 alternative fragment length(s) may be 291 bps INFO @ Thu, 09 Dec 2021 04:47:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9567166/SRX9567166.20_model.r WARNING @ Thu, 09 Dec 2021 04:47:14: #2 Since the d (291) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:47:14: #2 You may need to consider one of the other alternative d(s): 291 WARNING @ Thu, 09 Dec 2021 04:47:14: #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 04:47:14: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:47:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:47:20: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:47:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9567166/SRX9567166.20_peaks.xls INFO @ Thu, 09 Dec 2021 04:47:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9567166/SRX9567166.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:47:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9567166/SRX9567166.20_summits.bed INFO @ Thu, 09 Dec 2021 04:47:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (385 records, 4 fields): 3 millis CompletedMACS2peakCalling