Job ID = 12265321 SRX = SRX7246272 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: 00:14:21 13018833 reads; of these: 13018833 (100.00%) were paired; of these: 711078 (5.46%) aligned concordantly 0 times 10956427 (84.16%) aligned concordantly exactly 1 time 1351328 (10.38%) aligned concordantly >1 times ---- 711078 pairs aligned concordantly 0 times; of these: 137762 (19.37%) aligned discordantly 1 time ---- 573316 pairs aligned 0 times concordantly or discordantly; of these: 1146632 mates make up the pairs; of these: 912876 (79.61%) aligned 0 times 173801 (15.16%) aligned exactly 1 time 59955 (5.23%) aligned >1 times 96.49% overall alignment rate Time searching: 00:14:22 Overall time: 00:14:22 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] 3407924 / 8111074 = 0.4202 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:02:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7246272/SRX7246272.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7246272/SRX7246272.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7246272/SRX7246272.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7246272/SRX7246272.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, 03 Apr 2021 07:02:08: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:02:08: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:02:14: 1000000 INFO @ Sat, 03 Apr 2021 07:02:20: 2000000 INFO @ Sat, 03 Apr 2021 07:02:26: 3000000 INFO @ Sat, 03 Apr 2021 07:02:32: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:02:37: 5000000 INFO @ Sat, 03 Apr 2021 07:02:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7246272/SRX7246272.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7246272/SRX7246272.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7246272/SRX7246272.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7246272/SRX7246272.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, 03 Apr 2021 07:02:38: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:02:38: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:02:43: 6000000 INFO @ Sat, 03 Apr 2021 07:02:45: 1000000 INFO @ Sat, 03 Apr 2021 07:02:49: 7000000 INFO @ Sat, 03 Apr 2021 07:02:51: 2000000 INFO @ Sat, 03 Apr 2021 07:02:56: 8000000 INFO @ Sat, 03 Apr 2021 07:02:57: 3000000 INFO @ Sat, 03 Apr 2021 07:03:02: 9000000 INFO @ Sat, 03 Apr 2021 07:03:03: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:03:08: 10000000 INFO @ Sat, 03 Apr 2021 07:03:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7246272/SRX7246272.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7246272/SRX7246272.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7246272/SRX7246272.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7246272/SRX7246272.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, 03 Apr 2021 07:03:08: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:03:08: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:03:09: 5000000 INFO @ Sat, 03 Apr 2021 07:03:14: 11000000 INFO @ Sat, 03 Apr 2021 07:03:14: 1000000 INFO @ Sat, 03 Apr 2021 07:03:15: 6000000 INFO @ Sat, 03 Apr 2021 07:03:20: 2000000 INFO @ Sat, 03 Apr 2021 07:03:20: 12000000 INFO @ Sat, 03 Apr 2021 07:03:21: 7000000 INFO @ Sat, 03 Apr 2021 07:03:26: 3000000 INFO @ Sat, 03 Apr 2021 07:03:27: 13000000 INFO @ Sat, 03 Apr 2021 07:03:28: 8000000 INFO @ Sat, 03 Apr 2021 07:03:32: 4000000 INFO @ Sat, 03 Apr 2021 07:03:33: 14000000 INFO @ Sat, 03 Apr 2021 07:03:34: 9000000 INFO @ Sat, 03 Apr 2021 07:03:38: 5000000 INFO @ Sat, 03 Apr 2021 07:03:39: 15000000 INFO @ Sat, 03 Apr 2021 07:03:40: 10000000 INFO @ Sat, 03 Apr 2021 07:03:43: 6000000 INFO @ Sat, 03 Apr 2021 07:03:45: 16000000 INFO @ Sat, 03 Apr 2021 07:03:46: 11000000 INFO @ Sat, 03 Apr 2021 07:03:49: 7000000 INFO @ Sat, 03 Apr 2021 07:03:51: 17000000 INFO @ Sat, 03 Apr 2021 07:03:53: 12000000 INFO @ Sat, 03 Apr 2021 07:03:55: 8000000 INFO @ Sat, 03 Apr 2021 07:03:57: 18000000 INFO @ Sat, 03 Apr 2021 07:03:59: #1 tag size is determined as 96 bps INFO @ Sat, 03 Apr 2021 07:03:59: #1 tag size = 96 INFO @ Sat, 03 Apr 2021 07:03:59: #1 total tags in treatment: 8903949 INFO @ Sat, 03 Apr 2021 07:03:59: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:03:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:03:59: 13000000 INFO @ Sat, 03 Apr 2021 07:03:59: #1 tags after filtering in treatment: 5463210 INFO @ Sat, 03 Apr 2021 07:03:59: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 03 Apr 2021 07:03:59: #1 finished! INFO @ Sat, 03 Apr 2021 07:03:59: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:03:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:03:59: #2 number of paired peaks: 1568 INFO @ Sat, 03 Apr 2021 07:03:59: start model_add_line... INFO @ Sat, 03 Apr 2021 07:03:59: start X-correlation... INFO @ Sat, 03 Apr 2021 07:03:59: end of X-cor INFO @ Sat, 03 Apr 2021 07:03:59: #2 finished! INFO @ Sat, 03 Apr 2021 07:03:59: #2 predicted fragment length is 109 bps INFO @ Sat, 03 Apr 2021 07:03:59: #2 alternative fragment length(s) may be 109 bps INFO @ Sat, 03 Apr 2021 07:03:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7246272/SRX7246272.05_model.r WARNING @ Sat, 03 Apr 2021 07:03:59: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:03:59: #2 You may need to consider one of the other alternative d(s): 109 WARNING @ Sat, 03 Apr 2021 07:03:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:03:59: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:03:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:04:01: 9000000 INFO @ Sat, 03 Apr 2021 07:04:05: 14000000 INFO @ Sat, 03 Apr 2021 07:04:07: 10000000 INFO @ Sat, 03 Apr 2021 07:04:10: 15000000 INFO @ Sat, 03 Apr 2021 07:04:13: 11000000 INFO @ Sat, 03 Apr 2021 07:04:13: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:04:16: 16000000 INFO @ Sat, 03 Apr 2021 07:04:19: 12000000 INFO @ Sat, 03 Apr 2021 07:04:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7246272/SRX7246272.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:04:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7246272/SRX7246272.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:04:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7246272/SRX7246272.05_summits.bed INFO @ Sat, 03 Apr 2021 07:04:21: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5875 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:04:22: 17000000 INFO @ Sat, 03 Apr 2021 07:04:25: 13000000 INFO @ Sat, 03 Apr 2021 07:04:27: 18000000 INFO @ Sat, 03 Apr 2021 07:04:29: #1 tag size is determined as 96 bps INFO @ Sat, 03 Apr 2021 07:04:29: #1 tag size = 96 INFO @ Sat, 03 Apr 2021 07:04:29: #1 total tags in treatment: 8903949 INFO @ Sat, 03 Apr 2021 07:04:29: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:04:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:04:30: #1 tags after filtering in treatment: 5463210 INFO @ Sat, 03 Apr 2021 07:04:30: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 03 Apr 2021 07:04:30: #1 finished! INFO @ Sat, 03 Apr 2021 07:04:30: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:04:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:04:30: #2 number of paired peaks: 1568 INFO @ Sat, 03 Apr 2021 07:04:30: start model_add_line... INFO @ Sat, 03 Apr 2021 07:04:30: start X-correlation... INFO @ Sat, 03 Apr 2021 07:04:30: end of X-cor INFO @ Sat, 03 Apr 2021 07:04:30: #2 finished! INFO @ Sat, 03 Apr 2021 07:04:30: #2 predicted fragment length is 109 bps INFO @ Sat, 03 Apr 2021 07:04:30: #2 alternative fragment length(s) may be 109 bps INFO @ Sat, 03 Apr 2021 07:04:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7246272/SRX7246272.10_model.r WARNING @ Sat, 03 Apr 2021 07:04:30: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:04:30: #2 You may need to consider one of the other alternative d(s): 109 WARNING @ Sat, 03 Apr 2021 07:04:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:04:30: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:04:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:04:30: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:04:36: 15000000 INFO @ Sat, 03 Apr 2021 07:04:42: 16000000 INFO @ Sat, 03 Apr 2021 07:04:45: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:04:48: 17000000 INFO @ Sat, 03 Apr 2021 07:04:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7246272/SRX7246272.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:04:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7246272/SRX7246272.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:04:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7246272/SRX7246272.10_summits.bed INFO @ Sat, 03 Apr 2021 07:04:52: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3912 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:04:53: 18000000 INFO @ Sat, 03 Apr 2021 07:04:55: #1 tag size is determined as 96 bps INFO @ Sat, 03 Apr 2021 07:04:55: #1 tag size = 96 INFO @ Sat, 03 Apr 2021 07:04:55: #1 total tags in treatment: 8903949 INFO @ Sat, 03 Apr 2021 07:04:55: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:04:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:04:55: #1 tags after filtering in treatment: 5463210 INFO @ Sat, 03 Apr 2021 07:04:55: #1 Redundant rate of treatment: 0.39 INFO @ Sat, 03 Apr 2021 07:04:55: #1 finished! INFO @ Sat, 03 Apr 2021 07:04:55: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:04:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:04:55: #2 number of paired peaks: 1568 INFO @ Sat, 03 Apr 2021 07:04:55: start model_add_line... INFO @ Sat, 03 Apr 2021 07:04:55: start X-correlation... INFO @ Sat, 03 Apr 2021 07:04:55: end of X-cor INFO @ Sat, 03 Apr 2021 07:04:55: #2 finished! INFO @ Sat, 03 Apr 2021 07:04:55: #2 predicted fragment length is 109 bps INFO @ Sat, 03 Apr 2021 07:04:55: #2 alternative fragment length(s) may be 109 bps INFO @ Sat, 03 Apr 2021 07:04:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7246272/SRX7246272.20_model.r WARNING @ Sat, 03 Apr 2021 07:04:56: #2 Since the d (109) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:04:56: #2 You may need to consider one of the other alternative d(s): 109 WARNING @ Sat, 03 Apr 2021 07:04:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:04:56: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:04:56: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:05:09: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:05:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7246272/SRX7246272.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:05:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7246272/SRX7246272.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:05:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7246272/SRX7246272.20_summits.bed INFO @ Sat, 03 Apr 2021 07:05:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2046 records, 4 fields): 4 millis CompletedMACS2peakCalling