Job ID = 8070372 SRX = SRX8392417 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: 00:14:26 8367369 reads; of these: 8367369 (100.00%) were paired; of these: 1435100 (17.15%) aligned concordantly 0 times 6060387 (72.43%) aligned concordantly exactly 1 time 871882 (10.42%) aligned concordantly >1 times ---- 1435100 pairs aligned concordantly 0 times; of these: 559836 (39.01%) aligned discordantly 1 time ---- 875264 pairs aligned 0 times concordantly or discordantly; of these: 1750528 mates make up the pairs; of these: 1528645 (87.32%) aligned 0 times 98207 (5.61%) aligned exactly 1 time 123676 (7.07%) aligned >1 times 90.87% overall alignment rate Time searching: 00:14:26 Overall time: 00:14:26 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] 1708790 / 7450201 = 0.2294 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 08 Aug 2020 13:24:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392417/SRX8392417.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392417/SRX8392417.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392417/SRX8392417.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392417/SRX8392417.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 @ Sat, 08 Aug 2020 13:24:12: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:24:12: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:24:22: 1000000 INFO @ Sat, 08 Aug 2020 13:24:31: 2000000 INFO @ Sat, 08 Aug 2020 13:24:40: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 08 Aug 2020 13:24:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392417/SRX8392417.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392417/SRX8392417.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392417/SRX8392417.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392417/SRX8392417.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 @ Sat, 08 Aug 2020 13:24:42: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:24:42: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:24:51: 4000000 INFO @ Sat, 08 Aug 2020 13:24:53: 1000000 INFO @ Sat, 08 Aug 2020 13:25:01: 5000000 INFO @ Sat, 08 Aug 2020 13:25:04: 2000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 08 Aug 2020 13:25:12: 6000000 INFO @ Sat, 08 Aug 2020 13:25:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392417/SRX8392417.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392417/SRX8392417.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392417/SRX8392417.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392417/SRX8392417.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 @ Sat, 08 Aug 2020 13:25:12: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:25:12: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:25:15: 3000000 INFO @ Sat, 08 Aug 2020 13:25:23: 7000000 INFO @ Sat, 08 Aug 2020 13:25:24: 1000000 INFO @ Sat, 08 Aug 2020 13:25:26: 4000000 INFO @ Sat, 08 Aug 2020 13:25:33: 8000000 INFO @ Sat, 08 Aug 2020 13:25:35: 2000000 INFO @ Sat, 08 Aug 2020 13:25:39: 5000000 INFO @ Sat, 08 Aug 2020 13:25:44: 9000000 INFO @ Sat, 08 Aug 2020 13:25:47: 3000000 INFO @ Sat, 08 Aug 2020 13:25:51: 6000000 INFO @ Sat, 08 Aug 2020 13:25:55: 10000000 INFO @ Sat, 08 Aug 2020 13:25:59: 4000000 INFO @ Sat, 08 Aug 2020 13:26:04: 7000000 INFO @ Sat, 08 Aug 2020 13:26:06: 11000000 INFO @ Sat, 08 Aug 2020 13:26:10: 5000000 INFO @ Sat, 08 Aug 2020 13:26:14: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:26:14: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:26:14: #1 total tags in treatment: 5296534 INFO @ Sat, 08 Aug 2020 13:26:14: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:26:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:26:14: #1 tags after filtering in treatment: 4779081 INFO @ Sat, 08 Aug 2020 13:26:14: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 13:26:14: #1 finished! INFO @ Sat, 08 Aug 2020 13:26:14: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:26:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:26:15: #2 number of paired peaks: 1036 INFO @ Sat, 08 Aug 2020 13:26:15: start model_add_line... INFO @ Sat, 08 Aug 2020 13:26:15: start X-correlation... INFO @ Sat, 08 Aug 2020 13:26:15: end of X-cor INFO @ Sat, 08 Aug 2020 13:26:15: #2 finished! INFO @ Sat, 08 Aug 2020 13:26:15: #2 predicted fragment length is 203 bps INFO @ Sat, 08 Aug 2020 13:26:15: #2 alternative fragment length(s) may be 203 bps INFO @ Sat, 08 Aug 2020 13:26:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392417/SRX8392417.05_model.r WARNING @ Sat, 08 Aug 2020 13:26:15: #2 Since the d (203) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:26:15: #2 You may need to consider one of the other alternative d(s): 203 WARNING @ Sat, 08 Aug 2020 13:26:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 13:26:15: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:26:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:26:16: 8000000 INFO @ Sat, 08 Aug 2020 13:26:20: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 13:26:26: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:26:28: 9000000 INFO @ Sat, 08 Aug 2020 13:26:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392417/SRX8392417.05_peaks.xls INFO @ Sat, 08 Aug 2020 13:26:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392417/SRX8392417.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:26:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392417/SRX8392417.05_summits.bed INFO @ Sat, 08 Aug 2020 13:26:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5243 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:26:31: 7000000 INFO @ Sat, 08 Aug 2020 13:26:41: 10000000 INFO @ Sat, 08 Aug 2020 13:26:41: 8000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:26:52: 9000000 INFO @ Sat, 08 Aug 2020 13:26:53: 11000000 INFO @ Sat, 08 Aug 2020 13:27:02: 10000000 INFO @ Sat, 08 Aug 2020 13:27:02: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:27:02: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:27:02: #1 total tags in treatment: 5296534 INFO @ Sat, 08 Aug 2020 13:27:02: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:27:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:27:02: #1 tags after filtering in treatment: 4779081 INFO @ Sat, 08 Aug 2020 13:27:02: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 13:27:02: #1 finished! INFO @ Sat, 08 Aug 2020 13:27:02: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:27:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:27:03: #2 number of paired peaks: 1036 INFO @ Sat, 08 Aug 2020 13:27:03: start model_add_line... INFO @ Sat, 08 Aug 2020 13:27:03: start X-correlation... INFO @ Sat, 08 Aug 2020 13:27:03: end of X-cor INFO @ Sat, 08 Aug 2020 13:27:03: #2 finished! INFO @ Sat, 08 Aug 2020 13:27:03: #2 predicted fragment length is 203 bps INFO @ Sat, 08 Aug 2020 13:27:03: #2 alternative fragment length(s) may be 203 bps INFO @ Sat, 08 Aug 2020 13:27:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392417/SRX8392417.10_model.r WARNING @ Sat, 08 Aug 2020 13:27:03: #2 Since the d (203) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:27:03: #2 You may need to consider one of the other alternative d(s): 203 WARNING @ Sat, 08 Aug 2020 13:27:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 13:27:03: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:27:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:27:12: 11000000 INFO @ Sat, 08 Aug 2020 13:27:14: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:27:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392417/SRX8392417.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:27:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392417/SRX8392417.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:27:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392417/SRX8392417.10_summits.bed INFO @ Sat, 08 Aug 2020 13:27:19: Done! INFO @ Sat, 08 Aug 2020 13:27:19: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:27:19: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:27:19: #1 total tags in treatment: 5296534 INFO @ Sat, 08 Aug 2020 13:27:19: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:27:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2691 records, 4 fields): 3 millis INFO @ Sat, 08 Aug 2020 13:27:19: #1 tags after filtering in treatment: 4779081 CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:27:19: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 13:27:19: #1 finished! INFO @ Sat, 08 Aug 2020 13:27:19: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:27:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:27:19: #2 number of paired peaks: 1036 INFO @ Sat, 08 Aug 2020 13:27:19: start model_add_line... INFO @ Sat, 08 Aug 2020 13:27:19: start X-correlation... INFO @ Sat, 08 Aug 2020 13:27:19: end of X-cor INFO @ Sat, 08 Aug 2020 13:27:19: #2 finished! INFO @ Sat, 08 Aug 2020 13:27:19: #2 predicted fragment length is 203 bps INFO @ Sat, 08 Aug 2020 13:27:19: #2 alternative fragment length(s) may be 203 bps INFO @ Sat, 08 Aug 2020 13:27:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392417/SRX8392417.20_model.r WARNING @ Sat, 08 Aug 2020 13:27:19: #2 Since the d (203) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:27:19: #2 You may need to consider one of the other alternative d(s): 203 WARNING @ Sat, 08 Aug 2020 13:27:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 13:27:19: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:27:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:27:30: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:27:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392417/SRX8392417.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:27:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392417/SRX8392417.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:27:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392417/SRX8392417.20_summits.bed INFO @ Sat, 08 Aug 2020 13:27:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1005 records, 4 fields): 2 millis CompletedMACS2peakCalling