Job ID = 14159032 SRX = SRX10641182 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: 00:17:17 18371522 reads; of these: 18371522 (100.00%) were paired; of these: 13749663 (74.84%) aligned concordantly 0 times 4057452 (22.09%) aligned concordantly exactly 1 time 564407 (3.07%) aligned concordantly >1 times ---- 13749663 pairs aligned concordantly 0 times; of these: 2487044 (18.09%) aligned discordantly 1 time ---- 11262619 pairs aligned 0 times concordantly or discordantly; of these: 22525238 mates make up the pairs; of these: 21300160 (94.56%) aligned 0 times 719624 (3.19%) aligned exactly 1 time 505454 (2.24%) aligned >1 times 42.03% overall alignment rate Time searching: 00:17:17 Overall time: 00:17:17 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] 861145 / 7093848 = 0.1214 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 19:00:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641182/SRX10641182.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641182/SRX10641182.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641182/SRX10641182.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641182/SRX10641182.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 19:00:31: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:00:31: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:00:38: 1000000 INFO @ Wed, 08 Dec 2021 19:00:46: 2000000 INFO @ Wed, 08 Dec 2021 19:00:53: 3000000 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 19:01:01: 4000000 INFO @ Wed, 08 Dec 2021 19:01:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641182/SRX10641182.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641182/SRX10641182.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641182/SRX10641182.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641182/SRX10641182.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 19:01:01: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:01:01: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:01:07: 1000000 INFO @ Wed, 08 Dec 2021 19:01:08: 5000000 INFO @ Wed, 08 Dec 2021 19:01:14: 2000000 INFO @ Wed, 08 Dec 2021 19:01:16: 6000000 INFO @ Wed, 08 Dec 2021 19:01:20: 3000000 INFO @ Wed, 08 Dec 2021 19:01:23: 7000000 INFO @ Wed, 08 Dec 2021 19:01:27: 4000000 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 19:01:31: 8000000 INFO @ Wed, 08 Dec 2021 19:01:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641182/SRX10641182.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641182/SRX10641182.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641182/SRX10641182.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641182/SRX10641182.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 19:01:31: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:01:31: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:01:33: 5000000 INFO @ Wed, 08 Dec 2021 19:01:38: 9000000 INFO @ Wed, 08 Dec 2021 19:01:38: 1000000 INFO @ Wed, 08 Dec 2021 19:01:39: 6000000 INFO @ Wed, 08 Dec 2021 19:01:46: 7000000 INFO @ Wed, 08 Dec 2021 19:01:46: 2000000 INFO @ Wed, 08 Dec 2021 19:01:46: 10000000 INFO @ Wed, 08 Dec 2021 19:01:52: 8000000 INFO @ Wed, 08 Dec 2021 19:01:53: 3000000 INFO @ Wed, 08 Dec 2021 19:01:53: 11000000 INFO @ Wed, 08 Dec 2021 19:01:59: 9000000 INFO @ Wed, 08 Dec 2021 19:02:01: 4000000 INFO @ Wed, 08 Dec 2021 19:02:01: 12000000 INFO @ Wed, 08 Dec 2021 19:02:05: 10000000 INFO @ Wed, 08 Dec 2021 19:02:08: 5000000 INFO @ Wed, 08 Dec 2021 19:02:09: 13000000 INFO @ Wed, 08 Dec 2021 19:02:12: 11000000 INFO @ Wed, 08 Dec 2021 19:02:14: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 19:02:14: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 19:02:14: #1 total tags in treatment: 3996949 INFO @ Wed, 08 Dec 2021 19:02:14: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:02:14: #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 19:02:14: #1 tags after filtering in treatment: 3795920 INFO @ Wed, 08 Dec 2021 19:02:14: #1 Redundant rate of treatment: 0.05 INFO @ Wed, 08 Dec 2021 19:02:14: #1 finished! INFO @ Wed, 08 Dec 2021 19:02:14: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:02:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:02:14: #2 number of paired peaks: 1495 INFO @ Wed, 08 Dec 2021 19:02:14: start model_add_line... INFO @ Wed, 08 Dec 2021 19:02:15: start X-correlation... INFO @ Wed, 08 Dec 2021 19:02:15: end of X-cor INFO @ Wed, 08 Dec 2021 19:02:15: #2 finished! INFO @ Wed, 08 Dec 2021 19:02:15: #2 predicted fragment length is 252 bps INFO @ Wed, 08 Dec 2021 19:02:15: #2 alternative fragment length(s) may be 252 bps INFO @ Wed, 08 Dec 2021 19:02:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641182/SRX10641182.05_model.r WARNING @ Wed, 08 Dec 2021 19:02:15: #2 Since the d (252) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 19:02:15: #2 You may need to consider one of the other alternative d(s): 252 WARNING @ Wed, 08 Dec 2021 19:02:15: #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 19:02:15: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:02:15: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:02:16: 6000000 INFO @ Wed, 08 Dec 2021 19:02:18: 12000000 INFO @ Wed, 08 Dec 2021 19:02:23: 7000000 INFO @ Wed, 08 Dec 2021 19:02:24: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:02:24: 13000000 INFO @ Wed, 08 Dec 2021 19:02:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641182/SRX10641182.05_peaks.xls INFO @ Wed, 08 Dec 2021 19:02:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641182/SRX10641182.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:02:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641182/SRX10641182.05_summits.bed INFO @ Wed, 08 Dec 2021 19:02:28: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1131 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 19:02:29: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 19:02:29: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 19:02:29: #1 total tags in treatment: 3996949 INFO @ Wed, 08 Dec 2021 19:02:29: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:02:29: #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 19:02:29: #1 tags after filtering in treatment: 3795920 INFO @ Wed, 08 Dec 2021 19:02:29: #1 Redundant rate of treatment: 0.05 INFO @ Wed, 08 Dec 2021 19:02:29: #1 finished! INFO @ Wed, 08 Dec 2021 19:02:29: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:02:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:02:29: #2 number of paired peaks: 1495 INFO @ Wed, 08 Dec 2021 19:02:29: start model_add_line... INFO @ Wed, 08 Dec 2021 19:02:30: start X-correlation... INFO @ Wed, 08 Dec 2021 19:02:30: end of X-cor INFO @ Wed, 08 Dec 2021 19:02:30: #2 finished! INFO @ Wed, 08 Dec 2021 19:02:30: #2 predicted fragment length is 252 bps INFO @ Wed, 08 Dec 2021 19:02:30: #2 alternative fragment length(s) may be 252 bps INFO @ Wed, 08 Dec 2021 19:02:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641182/SRX10641182.10_model.r WARNING @ Wed, 08 Dec 2021 19:02:30: #2 Since the d (252) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 19:02:30: #2 You may need to consider one of the other alternative d(s): 252 WARNING @ Wed, 08 Dec 2021 19:02:30: #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 19:02:30: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:02:30: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:02:31: 8000000 INFO @ Wed, 08 Dec 2021 19:02:38: 9000000 INFO @ Wed, 08 Dec 2021 19:02:39: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:02:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641182/SRX10641182.10_peaks.xls INFO @ Wed, 08 Dec 2021 19:02:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641182/SRX10641182.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:02:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641182/SRX10641182.10_summits.bed INFO @ Wed, 08 Dec 2021 19:02:43: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (533 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 19:02:45: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 19:02:53: 11000000 INFO @ Wed, 08 Dec 2021 19:03:00: 12000000 INFO @ Wed, 08 Dec 2021 19:03:07: 13000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 19:03:13: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 19:03:13: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 19:03:13: #1 total tags in treatment: 3996949 INFO @ Wed, 08 Dec 2021 19:03:13: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:03:13: #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 19:03:13: #1 tags after filtering in treatment: 3795920 INFO @ Wed, 08 Dec 2021 19:03:13: #1 Redundant rate of treatment: 0.05 INFO @ Wed, 08 Dec 2021 19:03:13: #1 finished! INFO @ Wed, 08 Dec 2021 19:03:13: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:03:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:03:13: #2 number of paired peaks: 1495 INFO @ Wed, 08 Dec 2021 19:03:13: start model_add_line... INFO @ Wed, 08 Dec 2021 19:03:13: start X-correlation... INFO @ Wed, 08 Dec 2021 19:03:13: end of X-cor INFO @ Wed, 08 Dec 2021 19:03:13: #2 finished! INFO @ Wed, 08 Dec 2021 19:03:13: #2 predicted fragment length is 252 bps INFO @ Wed, 08 Dec 2021 19:03:13: #2 alternative fragment length(s) may be 252 bps INFO @ Wed, 08 Dec 2021 19:03:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641182/SRX10641182.20_model.r WARNING @ Wed, 08 Dec 2021 19:03:13: #2 Since the d (252) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 19:03:13: #2 You may need to consider one of the other alternative d(s): 252 WARNING @ Wed, 08 Dec 2021 19:03:13: #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 19:03:13: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:03:13: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:03:23: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:03:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641182/SRX10641182.20_peaks.xls INFO @ Wed, 08 Dec 2021 19:03:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641182/SRX10641182.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:03:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641182/SRX10641182.20_summits.bed INFO @ Wed, 08 Dec 2021 19:03:27: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (283 records, 4 fields): 2 millis CompletedMACS2peakCalling