Job ID = 14160469 SRX = SRX9567204 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: 00:22:58 11560982 reads; of these: 11560982 (100.00%) were paired; of these: 4490787 (38.84%) aligned concordantly 0 times 6199204 (53.62%) aligned concordantly exactly 1 time 870991 (7.53%) aligned concordantly >1 times ---- 4490787 pairs aligned concordantly 0 times; of these: 3174046 (70.68%) aligned discordantly 1 time ---- 1316741 pairs aligned 0 times concordantly or discordantly; of these: 2633482 mates make up the pairs; of these: 1256223 (47.70%) aligned 0 times 634576 (24.10%) aligned exactly 1 time 742683 (28.20%) aligned >1 times 94.57% overall alignment rate Time searching: 00:22:58 Overall time: 00:22:58 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 16 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] 8341349 / 10240344 = 0.8146 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 03:10:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9567204/SRX9567204.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9567204/SRX9567204.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9567204/SRX9567204.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9567204/SRX9567204.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 03:10:33: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:10:33: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:10:44: 1000000 INFO @ Thu, 09 Dec 2021 03:10:54: 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 03:11:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9567204/SRX9567204.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9567204/SRX9567204.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9567204/SRX9567204.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9567204/SRX9567204.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 03:11:04: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:11:04: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:11:05: 3000000 INFO @ Thu, 09 Dec 2021 03:11:16: 1000000 INFO @ Thu, 09 Dec 2021 03:11:17: 4000000 INFO @ Thu, 09 Dec 2021 03:11:28: 2000000 INFO @ Thu, 09 Dec 2021 03:11:29: 5000000 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 03:11:31: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:11:31: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:11:31: #1 total tags in treatment: 1326956 INFO @ Thu, 09 Dec 2021 03:11:31: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:11:31: #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 03:11:32: #1 tags after filtering in treatment: 1235090 INFO @ Thu, 09 Dec 2021 03:11:32: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 09 Dec 2021 03:11:32: #1 finished! INFO @ Thu, 09 Dec 2021 03:11:32: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:11:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:11:32: #2 number of paired peaks: 2116 INFO @ Thu, 09 Dec 2021 03:11:32: start model_add_line... INFO @ Thu, 09 Dec 2021 03:11:32: start X-correlation... INFO @ Thu, 09 Dec 2021 03:11:32: end of X-cor INFO @ Thu, 09 Dec 2021 03:11:32: #2 finished! INFO @ Thu, 09 Dec 2021 03:11:32: #2 predicted fragment length is 258 bps INFO @ Thu, 09 Dec 2021 03:11:32: #2 alternative fragment length(s) may be 258 bps INFO @ Thu, 09 Dec 2021 03:11:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9567204/SRX9567204.05_model.r WARNING @ Thu, 09 Dec 2021 03:11:32: #2 Since the d (258) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:11:32: #2 You may need to consider one of the other alternative d(s): 258 WARNING @ Thu, 09 Dec 2021 03:11:32: #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 03:11:32: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:11:32: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:11:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9567204/SRX9567204.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9567204/SRX9567204.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9567204/SRX9567204.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9567204/SRX9567204.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 03:11:33: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:11:33: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:11:35: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:11:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9567204/SRX9567204.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:11:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9567204/SRX9567204.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:11:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9567204/SRX9567204.05_summits.bed INFO @ Thu, 09 Dec 2021 03:11:37: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (696 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:11:40: 3000000 INFO @ Thu, 09 Dec 2021 03:11:45: 1000000 INFO @ Thu, 09 Dec 2021 03:11:53: 4000000 INFO @ Thu, 09 Dec 2021 03:11:58: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:12:06: 5000000 INFO @ Thu, 09 Dec 2021 03:12:08: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:12:08: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:12:08: #1 total tags in treatment: 1326956 INFO @ Thu, 09 Dec 2021 03:12:08: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:12:08: #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 03:12:08: #1 tags after filtering in treatment: 1235090 INFO @ Thu, 09 Dec 2021 03:12:08: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 09 Dec 2021 03:12:08: #1 finished! INFO @ Thu, 09 Dec 2021 03:12:08: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:12:08: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:12:08: #2 number of paired peaks: 2116 INFO @ Thu, 09 Dec 2021 03:12:08: start model_add_line... INFO @ Thu, 09 Dec 2021 03:12:08: start X-correlation... INFO @ Thu, 09 Dec 2021 03:12:08: end of X-cor INFO @ Thu, 09 Dec 2021 03:12:08: #2 finished! INFO @ Thu, 09 Dec 2021 03:12:08: #2 predicted fragment length is 258 bps INFO @ Thu, 09 Dec 2021 03:12:08: #2 alternative fragment length(s) may be 258 bps INFO @ Thu, 09 Dec 2021 03:12:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9567204/SRX9567204.10_model.r WARNING @ Thu, 09 Dec 2021 03:12:08: #2 Since the d (258) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:12:08: #2 You may need to consider one of the other alternative d(s): 258 WARNING @ Thu, 09 Dec 2021 03:12:08: #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 03:12:08: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:12:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:12:09: 3000000 INFO @ Thu, 09 Dec 2021 03:12:12: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:12:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9567204/SRX9567204.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:12:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9567204/SRX9567204.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:12:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9567204/SRX9567204.10_summits.bed INFO @ Thu, 09 Dec 2021 03:12:13: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (392 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:12:20: 4000000 INFO @ Thu, 09 Dec 2021 03:12:31: 5000000 INFO @ Thu, 09 Dec 2021 03:12:33: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:12:33: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:12:33: #1 total tags in treatment: 1326956 INFO @ Thu, 09 Dec 2021 03:12:33: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:12:33: #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 03:12:33: #1 tags after filtering in treatment: 1235090 INFO @ Thu, 09 Dec 2021 03:12:33: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 09 Dec 2021 03:12:33: #1 finished! INFO @ Thu, 09 Dec 2021 03:12:33: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:12:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:12:33: #2 number of paired peaks: 2116 INFO @ Thu, 09 Dec 2021 03:12:33: start model_add_line... INFO @ Thu, 09 Dec 2021 03:12:33: start X-correlation... INFO @ Thu, 09 Dec 2021 03:12:33: end of X-cor INFO @ Thu, 09 Dec 2021 03:12:33: #2 finished! INFO @ Thu, 09 Dec 2021 03:12:33: #2 predicted fragment length is 258 bps INFO @ Thu, 09 Dec 2021 03:12:33: #2 alternative fragment length(s) may be 258 bps INFO @ Thu, 09 Dec 2021 03:12:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9567204/SRX9567204.20_model.r WARNING @ Thu, 09 Dec 2021 03:12:33: #2 Since the d (258) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:12:33: #2 You may need to consider one of the other alternative d(s): 258 WARNING @ Thu, 09 Dec 2021 03:12:33: #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 03:12:33: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:12:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:12:37: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:12:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9567204/SRX9567204.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:12:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9567204/SRX9567204.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:12:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9567204/SRX9567204.20_summits.bed INFO @ Thu, 09 Dec 2021 03:12:38: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (203 records, 4 fields): 2 millis CompletedMACS2peakCalling