Job ID = 14159952 SRX = SRX8845651 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: 00:38:31 39634020 reads; of these: 39634020 (100.00%) were paired; of these: 20128667 (50.79%) aligned concordantly 0 times 16567432 (41.80%) aligned concordantly exactly 1 time 2937921 (7.41%) aligned concordantly >1 times ---- 20128667 pairs aligned concordantly 0 times; of these: 4114096 (20.44%) aligned discordantly 1 time ---- 16014571 pairs aligned 0 times concordantly or discordantly; of these: 32029142 mates make up the pairs; of these: 29313370 (91.52%) aligned 0 times 1215391 (3.79%) aligned exactly 1 time 1500381 (4.68%) aligned >1 times 63.02% overall alignment rate Time searching: 00:38:32 Overall time: 00:38:32 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] 20535932 / 23359765 = 0.8791 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 01:36:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845651/SRX8845651.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845651/SRX8845651.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845651/SRX8845651.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845651/SRX8845651.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 01:36:13: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:36:13: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:36:20: 1000000 INFO @ Thu, 09 Dec 2021 01:36:26: 2000000 INFO @ Thu, 09 Dec 2021 01:36:32: 3000000 INFO @ Thu, 09 Dec 2021 01:36:39: 4000000 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 01:36:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845651/SRX8845651.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845651/SRX8845651.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845651/SRX8845651.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845651/SRX8845651.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 01:36:42: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:36:42: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:36:46: 5000000 INFO @ Thu, 09 Dec 2021 01:36:49: 1000000 INFO @ Thu, 09 Dec 2021 01:36:54: 6000000 INFO @ Thu, 09 Dec 2021 01:36:56: 2000000 INFO @ Thu, 09 Dec 2021 01:37:01: 7000000 INFO @ Thu, 09 Dec 2021 01:37:03: 3000000 INFO @ Thu, 09 Dec 2021 01:37:09: 8000000 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 01:37:11: 4000000 INFO @ Thu, 09 Dec 2021 01:37:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845651/SRX8845651.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845651/SRX8845651.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845651/SRX8845651.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845651/SRX8845651.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 01:37:12: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:37:12: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:37:15: #1 tag size is determined as 73 bps INFO @ Thu, 09 Dec 2021 01:37:15: #1 tag size = 73 INFO @ Thu, 09 Dec 2021 01:37:15: #1 total tags in treatment: 2216158 INFO @ Thu, 09 Dec 2021 01:37:15: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:37:15: #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 01:37:15: #1 tags after filtering in treatment: 1522063 INFO @ Thu, 09 Dec 2021 01:37:15: #1 Redundant rate of treatment: 0.31 INFO @ Thu, 09 Dec 2021 01:37:15: #1 finished! INFO @ Thu, 09 Dec 2021 01:37:15: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:37:15: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:37:16: #2 number of paired peaks: 2619 INFO @ Thu, 09 Dec 2021 01:37:16: start model_add_line... INFO @ Thu, 09 Dec 2021 01:37:16: start X-correlation... INFO @ Thu, 09 Dec 2021 01:37:16: end of X-cor INFO @ Thu, 09 Dec 2021 01:37:16: #2 finished! INFO @ Thu, 09 Dec 2021 01:37:16: #2 predicted fragment length is 114 bps INFO @ Thu, 09 Dec 2021 01:37:16: #2 alternative fragment length(s) may be 114 bps INFO @ Thu, 09 Dec 2021 01:37:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845651/SRX8845651.05_model.r WARNING @ Thu, 09 Dec 2021 01:37:16: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:37:16: #2 You may need to consider one of the other alternative d(s): 114 WARNING @ Thu, 09 Dec 2021 01:37:16: #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 01:37:16: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:37:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:37:18: 5000000 INFO @ Thu, 09 Dec 2021 01:37:20: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:37:20: 1000000 INFO @ Thu, 09 Dec 2021 01:37:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845651/SRX8845651.05_peaks.xls INFO @ Thu, 09 Dec 2021 01:37:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845651/SRX8845651.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:37:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845651/SRX8845651.05_summits.bed INFO @ Thu, 09 Dec 2021 01:37:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3188 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 01:37:25: 6000000 INFO @ Thu, 09 Dec 2021 01:37:27: 2000000 INFO @ Thu, 09 Dec 2021 01:37:33: 7000000 INFO @ Thu, 09 Dec 2021 01:37:35: 3000000 INFO @ Thu, 09 Dec 2021 01:37:40: 8000000 INFO @ Thu, 09 Dec 2021 01:37:42: 4000000 INFO @ Thu, 09 Dec 2021 01:37:47: #1 tag size is determined as 73 bps INFO @ Thu, 09 Dec 2021 01:37:47: #1 tag size = 73 INFO @ Thu, 09 Dec 2021 01:37:47: #1 total tags in treatment: 2216158 INFO @ Thu, 09 Dec 2021 01:37:47: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:37:47: #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 01:37:47: #1 tags after filtering in treatment: 1522063 INFO @ Thu, 09 Dec 2021 01:37:47: #1 Redundant rate of treatment: 0.31 INFO @ Thu, 09 Dec 2021 01:37:47: #1 finished! INFO @ Thu, 09 Dec 2021 01:37:47: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:37:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:37:47: #2 number of paired peaks: 2619 INFO @ Thu, 09 Dec 2021 01:37:47: start model_add_line... INFO @ Thu, 09 Dec 2021 01:37:47: start X-correlation... INFO @ Thu, 09 Dec 2021 01:37:47: end of X-cor INFO @ Thu, 09 Dec 2021 01:37:47: #2 finished! INFO @ Thu, 09 Dec 2021 01:37:47: #2 predicted fragment length is 114 bps INFO @ Thu, 09 Dec 2021 01:37:47: #2 alternative fragment length(s) may be 114 bps INFO @ Thu, 09 Dec 2021 01:37:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845651/SRX8845651.10_model.r WARNING @ Thu, 09 Dec 2021 01:37:47: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:37:47: #2 You may need to consider one of the other alternative d(s): 114 WARNING @ Thu, 09 Dec 2021 01:37:47: #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 01:37:47: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:37:47: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:37:49: 5000000 INFO @ Thu, 09 Dec 2021 01:37:51: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:37:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845651/SRX8845651.10_peaks.xls INFO @ Thu, 09 Dec 2021 01:37:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845651/SRX8845651.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:37:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845651/SRX8845651.10_summits.bed INFO @ Thu, 09 Dec 2021 01:37:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1717 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 01:37:56: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 01:38:04: 7000000 INFO @ Thu, 09 Dec 2021 01:38:11: 8000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 01:38:17: #1 tag size is determined as 73 bps INFO @ Thu, 09 Dec 2021 01:38:17: #1 tag size = 73 INFO @ Thu, 09 Dec 2021 01:38:17: #1 total tags in treatment: 2216158 INFO @ Thu, 09 Dec 2021 01:38:17: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:38:17: #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 01:38:17: #1 tags after filtering in treatment: 1522063 INFO @ Thu, 09 Dec 2021 01:38:17: #1 Redundant rate of treatment: 0.31 INFO @ Thu, 09 Dec 2021 01:38:17: #1 finished! INFO @ Thu, 09 Dec 2021 01:38:17: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:38:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:38:17: #2 number of paired peaks: 2619 INFO @ Thu, 09 Dec 2021 01:38:17: start model_add_line... INFO @ Thu, 09 Dec 2021 01:38:17: start X-correlation... INFO @ Thu, 09 Dec 2021 01:38:17: end of X-cor INFO @ Thu, 09 Dec 2021 01:38:17: #2 finished! INFO @ Thu, 09 Dec 2021 01:38:17: #2 predicted fragment length is 114 bps INFO @ Thu, 09 Dec 2021 01:38:17: #2 alternative fragment length(s) may be 114 bps INFO @ Thu, 09 Dec 2021 01:38:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845651/SRX8845651.20_model.r WARNING @ Thu, 09 Dec 2021 01:38:17: #2 Since the d (114) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:38:17: #2 You may need to consider one of the other alternative d(s): 114 WARNING @ Thu, 09 Dec 2021 01:38:17: #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 01:38:17: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:38:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:38:21: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:38:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845651/SRX8845651.20_peaks.xls INFO @ Thu, 09 Dec 2021 01:38:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845651/SRX8845651.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:38:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845651/SRX8845651.20_summits.bed INFO @ Thu, 09 Dec 2021 01:38:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (618 records, 4 fields): 2 millis CompletedMACS2peakCalling