Job ID = 14159177 SRX = SRX10641191 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: 00:31:10 20176576 reads; of these: 20176576 (100.00%) were paired; of these: 14065278 (69.71%) aligned concordantly 0 times 3075944 (15.25%) aligned concordantly exactly 1 time 3035354 (15.04%) aligned concordantly >1 times ---- 14065278 pairs aligned concordantly 0 times; of these: 1258587 (8.95%) aligned discordantly 1 time ---- 12806691 pairs aligned 0 times concordantly or discordantly; of these: 25613382 mates make up the pairs; of these: 24817732 (96.89%) aligned 0 times 369874 (1.44%) aligned exactly 1 time 425776 (1.66%) aligned >1 times 38.50% overall alignment rate Time searching: 00:31:10 Overall time: 00:31:10 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 12 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] 1858477 / 7340306 = 0.2532 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 @ Wed, 08 Dec 2021 20:45:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641191/SRX10641191.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641191/SRX10641191.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641191/SRX10641191.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641191/SRX10641191.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 @ Wed, 08 Dec 2021 20:45:45: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:45:45: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:45:51: 1000000 INFO @ Wed, 08 Dec 2021 20:45:58: 2000000 INFO @ Wed, 08 Dec 2021 20:46:05: 3000000 INFO @ Wed, 08 Dec 2021 20:46:11: 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 @ Wed, 08 Dec 2021 20:46:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641191/SRX10641191.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641191/SRX10641191.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641191/SRX10641191.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641191/SRX10641191.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 @ Wed, 08 Dec 2021 20:46:15: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:46:15: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:46:18: 5000000 INFO @ Wed, 08 Dec 2021 20:46:24: 1000000 INFO @ Wed, 08 Dec 2021 20:46:25: 6000000 INFO @ Wed, 08 Dec 2021 20:46:32: 7000000 INFO @ Wed, 08 Dec 2021 20:46:32: 2000000 INFO @ Wed, 08 Dec 2021 20:46:39: 8000000 INFO @ Wed, 08 Dec 2021 20:46:39: 3000000 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 @ Wed, 08 Dec 2021 20:46:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641191/SRX10641191.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641191/SRX10641191.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641191/SRX10641191.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641191/SRX10641191.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 @ Wed, 08 Dec 2021 20:46:45: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:46:45: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:46:46: 9000000 INFO @ Wed, 08 Dec 2021 20:46:46: 4000000 INFO @ Wed, 08 Dec 2021 20:46:53: 1000000 INFO @ Wed, 08 Dec 2021 20:46:53: 10000000 INFO @ Wed, 08 Dec 2021 20:46:53: 5000000 INFO @ Wed, 08 Dec 2021 20:47:00: 11000000 INFO @ Wed, 08 Dec 2021 20:47:00: 6000000 INFO @ Wed, 08 Dec 2021 20:47:01: 2000000 INFO @ Wed, 08 Dec 2021 20:47:06: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 20:47:06: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 20:47:06: #1 total tags in treatment: 4391935 INFO @ Wed, 08 Dec 2021 20:47:06: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:47:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 20:47:06: #1 tags after filtering in treatment: 2987242 INFO @ Wed, 08 Dec 2021 20:47:06: #1 Redundant rate of treatment: 0.32 INFO @ Wed, 08 Dec 2021 20:47:06: #1 finished! INFO @ Wed, 08 Dec 2021 20:47:06: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:47:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:47:06: #2 number of paired peaks: 1185 INFO @ Wed, 08 Dec 2021 20:47:06: start model_add_line... INFO @ Wed, 08 Dec 2021 20:47:06: start X-correlation... INFO @ Wed, 08 Dec 2021 20:47:06: end of X-cor INFO @ Wed, 08 Dec 2021 20:47:06: #2 finished! INFO @ Wed, 08 Dec 2021 20:47:06: #2 predicted fragment length is 279 bps INFO @ Wed, 08 Dec 2021 20:47:06: #2 alternative fragment length(s) may be 279 bps INFO @ Wed, 08 Dec 2021 20:47:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641191/SRX10641191.05_model.r WARNING @ Wed, 08 Dec 2021 20:47:07: #2 Since the d (279) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:47:07: #2 You may need to consider one of the other alternative d(s): 279 WARNING @ Wed, 08 Dec 2021 20:47:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 20:47:07: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:47:07: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:47:07: 7000000 INFO @ Wed, 08 Dec 2021 20:47:09: 3000000 INFO @ Wed, 08 Dec 2021 20:47:14: 8000000 INFO @ Wed, 08 Dec 2021 20:47:15: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:47:17: 4000000 INFO @ Wed, 08 Dec 2021 20:47:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641191/SRX10641191.05_peaks.xls INFO @ Wed, 08 Dec 2021 20:47:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641191/SRX10641191.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:47:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641191/SRX10641191.05_summits.bed INFO @ Wed, 08 Dec 2021 20:47:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1235 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:47:21: 9000000 INFO @ Wed, 08 Dec 2021 20:47:25: 5000000 INFO @ Wed, 08 Dec 2021 20:47:28: 10000000 INFO @ Wed, 08 Dec 2021 20:47:33: 6000000 INFO @ Wed, 08 Dec 2021 20:47:36: 11000000 INFO @ Wed, 08 Dec 2021 20:47:41: 7000000 INFO @ Wed, 08 Dec 2021 20:47:42: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 20:47:42: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 20:47:42: #1 total tags in treatment: 4391935 INFO @ Wed, 08 Dec 2021 20:47:42: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:47:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 20:47:42: #1 tags after filtering in treatment: 2987242 INFO @ Wed, 08 Dec 2021 20:47:42: #1 Redundant rate of treatment: 0.32 INFO @ Wed, 08 Dec 2021 20:47:42: #1 finished! INFO @ Wed, 08 Dec 2021 20:47:42: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:47:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:47:42: #2 number of paired peaks: 1185 INFO @ Wed, 08 Dec 2021 20:47:42: start model_add_line... INFO @ Wed, 08 Dec 2021 20:47:42: start X-correlation... INFO @ Wed, 08 Dec 2021 20:47:42: end of X-cor INFO @ Wed, 08 Dec 2021 20:47:42: #2 finished! INFO @ Wed, 08 Dec 2021 20:47:42: #2 predicted fragment length is 279 bps INFO @ Wed, 08 Dec 2021 20:47:42: #2 alternative fragment length(s) may be 279 bps INFO @ Wed, 08 Dec 2021 20:47:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641191/SRX10641191.10_model.r WARNING @ Wed, 08 Dec 2021 20:47:42: #2 Since the d (279) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:47:42: #2 You may need to consider one of the other alternative d(s): 279 WARNING @ Wed, 08 Dec 2021 20:47:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 20:47:42: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:47:42: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 20:47:49: 8000000 INFO @ Wed, 08 Dec 2021 20:47:51: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:47:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641191/SRX10641191.10_peaks.xls INFO @ Wed, 08 Dec 2021 20:47:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641191/SRX10641191.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:47:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641191/SRX10641191.10_summits.bed INFO @ Wed, 08 Dec 2021 20:47:54: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (773 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:47:57: 9000000 INFO @ Wed, 08 Dec 2021 20:48:05: 10000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 20:48:13: 11000000 INFO @ Wed, 08 Dec 2021 20:48:19: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 20:48:19: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 20:48:19: #1 total tags in treatment: 4391935 INFO @ Wed, 08 Dec 2021 20:48:19: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:48:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 20:48:19: #1 tags after filtering in treatment: 2987242 INFO @ Wed, 08 Dec 2021 20:48:19: #1 Redundant rate of treatment: 0.32 INFO @ Wed, 08 Dec 2021 20:48:19: #1 finished! INFO @ Wed, 08 Dec 2021 20:48:19: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:48:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:48:19: #2 number of paired peaks: 1185 INFO @ Wed, 08 Dec 2021 20:48:19: start model_add_line... INFO @ Wed, 08 Dec 2021 20:48:19: start X-correlation... INFO @ Wed, 08 Dec 2021 20:48:19: end of X-cor INFO @ Wed, 08 Dec 2021 20:48:19: #2 finished! INFO @ Wed, 08 Dec 2021 20:48:19: #2 predicted fragment length is 279 bps INFO @ Wed, 08 Dec 2021 20:48:19: #2 alternative fragment length(s) may be 279 bps INFO @ Wed, 08 Dec 2021 20:48:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641191/SRX10641191.20_model.r WARNING @ Wed, 08 Dec 2021 20:48:19: #2 Since the d (279) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:48:19: #2 You may need to consider one of the other alternative d(s): 279 WARNING @ Wed, 08 Dec 2021 20:48:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 20:48:19: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:48:19: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:48:28: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:48:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641191/SRX10641191.20_peaks.xls INFO @ Wed, 08 Dec 2021 20:48:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641191/SRX10641191.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:48:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641191/SRX10641191.20_summits.bed INFO @ Wed, 08 Dec 2021 20:48:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (529 records, 4 fields): 2 millis CompletedMACS2peakCalling