Job ID = 14159668 SRX = SRX8845625 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: 00:06:10 7505545 reads; of these: 7505545 (100.00%) were paired; of these: 2909896 (38.77%) aligned concordantly 0 times 4079058 (54.35%) aligned concordantly exactly 1 time 516591 (6.88%) aligned concordantly >1 times ---- 2909896 pairs aligned concordantly 0 times; of these: 988835 (33.98%) aligned discordantly 1 time ---- 1921061 pairs aligned 0 times concordantly or discordantly; of these: 3842122 mates make up the pairs; of these: 3356369 (87.36%) aligned 0 times 262498 (6.83%) aligned exactly 1 time 223255 (5.81%) aligned >1 times 77.64% overall alignment rate Time searching: 00:06:10 Overall time: 00:06:10 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 8 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] 876719 / 5523115 = 0.1587 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 00:20:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845625/SRX8845625.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845625/SRX8845625.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845625/SRX8845625.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845625/SRX8845625.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 00:20:34: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:20:34: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:20:40: 1000000 INFO @ Thu, 09 Dec 2021 00:20:46: 2000000 INFO @ Thu, 09 Dec 2021 00:20:52: 3000000 INFO @ Thu, 09 Dec 2021 00:20:58: 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 00:21:04: 5000000 INFO @ Thu, 09 Dec 2021 00:21:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845625/SRX8845625.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845625/SRX8845625.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845625/SRX8845625.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845625/SRX8845625.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 00:21:04: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:21:04: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:21:10: 6000000 INFO @ Thu, 09 Dec 2021 00:21:11: 1000000 INFO @ Thu, 09 Dec 2021 00:21:16: 7000000 INFO @ Thu, 09 Dec 2021 00:21:17: 2000000 INFO @ Thu, 09 Dec 2021 00:21:22: 8000000 INFO @ Thu, 09 Dec 2021 00:21:23: 3000000 INFO @ Thu, 09 Dec 2021 00:21:29: 9000000 INFO @ Thu, 09 Dec 2021 00:21:29: 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 @ Thu, 09 Dec 2021 00:21:34: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 00:21:34: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 00:21:34: #1 total tags in treatment: 3908236 INFO @ Thu, 09 Dec 2021 00:21:34: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:21:34: #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 00:21:34: #1 tags after filtering in treatment: 2868600 INFO @ Thu, 09 Dec 2021 00:21:34: #1 Redundant rate of treatment: 0.27 INFO @ Thu, 09 Dec 2021 00:21:34: #1 finished! INFO @ Thu, 09 Dec 2021 00:21:34: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:21:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:21:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845625/SRX8845625.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845625/SRX8845625.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845625/SRX8845625.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845625/SRX8845625.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 00:21:34: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:21:34: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:21:34: #2 number of paired peaks: 3324 INFO @ Thu, 09 Dec 2021 00:21:34: start model_add_line... INFO @ Thu, 09 Dec 2021 00:21:34: start X-correlation... INFO @ Thu, 09 Dec 2021 00:21:34: end of X-cor INFO @ Thu, 09 Dec 2021 00:21:34: #2 finished! INFO @ Thu, 09 Dec 2021 00:21:34: #2 predicted fragment length is 110 bps INFO @ Thu, 09 Dec 2021 00:21:34: #2 alternative fragment length(s) may be 110 bps INFO @ Thu, 09 Dec 2021 00:21:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845625/SRX8845625.05_model.r WARNING @ Thu, 09 Dec 2021 00:21:34: #2 Since the d (110) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:21:34: #2 You may need to consider one of the other alternative d(s): 110 WARNING @ Thu, 09 Dec 2021 00:21:34: #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 00:21:34: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:21:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:21:35: 5000000 INFO @ Thu, 09 Dec 2021 00:21:40: 1000000 INFO @ Thu, 09 Dec 2021 00:21:41: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:21:41: 6000000 INFO @ Thu, 09 Dec 2021 00:21:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845625/SRX8845625.05_peaks.xls INFO @ Thu, 09 Dec 2021 00:21:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845625/SRX8845625.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:21:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845625/SRX8845625.05_summits.bed INFO @ Thu, 09 Dec 2021 00:21:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (7455 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:21:45: 2000000 INFO @ Thu, 09 Dec 2021 00:21:47: 7000000 INFO @ Thu, 09 Dec 2021 00:21:51: 3000000 INFO @ Thu, 09 Dec 2021 00:21:53: 8000000 INFO @ Thu, 09 Dec 2021 00:21:56: 4000000 INFO @ Thu, 09 Dec 2021 00:21:59: 9000000 INFO @ Thu, 09 Dec 2021 00:22:02: 5000000 INFO @ Thu, 09 Dec 2021 00:22:05: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 00:22:05: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 00:22:05: #1 total tags in treatment: 3908236 INFO @ Thu, 09 Dec 2021 00:22:05: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:22:05: #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 00:22:05: #1 tags after filtering in treatment: 2868600 INFO @ Thu, 09 Dec 2021 00:22:05: #1 Redundant rate of treatment: 0.27 INFO @ Thu, 09 Dec 2021 00:22:05: #1 finished! INFO @ Thu, 09 Dec 2021 00:22:05: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:22:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:22:05: #2 number of paired peaks: 3324 INFO @ Thu, 09 Dec 2021 00:22:05: start model_add_line... INFO @ Thu, 09 Dec 2021 00:22:05: start X-correlation... INFO @ Thu, 09 Dec 2021 00:22:05: end of X-cor INFO @ Thu, 09 Dec 2021 00:22:05: #2 finished! INFO @ Thu, 09 Dec 2021 00:22:05: #2 predicted fragment length is 110 bps INFO @ Thu, 09 Dec 2021 00:22:05: #2 alternative fragment length(s) may be 110 bps INFO @ Thu, 09 Dec 2021 00:22:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845625/SRX8845625.10_model.r WARNING @ Thu, 09 Dec 2021 00:22:05: #2 Since the d (110) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:22:05: #2 You may need to consider one of the other alternative d(s): 110 WARNING @ Thu, 09 Dec 2021 00:22:05: #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 00:22:05: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:22:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:22:07: 6000000 INFO @ Thu, 09 Dec 2021 00:22:12: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:22:12: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 00:22:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845625/SRX8845625.10_peaks.xls INFO @ Thu, 09 Dec 2021 00:22:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845625/SRX8845625.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:22:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845625/SRX8845625.10_summits.bed INFO @ Thu, 09 Dec 2021 00:22:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4832 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:22:17: 8000000 INFO @ Thu, 09 Dec 2021 00:22:22: 9000000 INFO @ Thu, 09 Dec 2021 00:22:27: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 00:22:27: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 00:22:27: #1 total tags in treatment: 3908236 INFO @ Thu, 09 Dec 2021 00:22:27: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:22:27: #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 00:22:27: #1 tags after filtering in treatment: 2868600 INFO @ Thu, 09 Dec 2021 00:22:27: #1 Redundant rate of treatment: 0.27 INFO @ Thu, 09 Dec 2021 00:22:27: #1 finished! INFO @ Thu, 09 Dec 2021 00:22:27: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:22:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:22:27: #2 number of paired peaks: 3324 INFO @ Thu, 09 Dec 2021 00:22:27: start model_add_line... INFO @ Thu, 09 Dec 2021 00:22:27: start X-correlation... INFO @ Thu, 09 Dec 2021 00:22:28: end of X-cor INFO @ Thu, 09 Dec 2021 00:22:28: #2 finished! INFO @ Thu, 09 Dec 2021 00:22:28: #2 predicted fragment length is 110 bps INFO @ Thu, 09 Dec 2021 00:22:28: #2 alternative fragment length(s) may be 110 bps INFO @ Thu, 09 Dec 2021 00:22:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845625/SRX8845625.20_model.r WARNING @ Thu, 09 Dec 2021 00:22:28: #2 Since the d (110) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:22:28: #2 You may need to consider one of the other alternative d(s): 110 WARNING @ Thu, 09 Dec 2021 00:22:28: #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 00:22:28: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:22:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 00:22:34: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:22:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845625/SRX8845625.20_peaks.xls INFO @ Thu, 09 Dec 2021 00:22:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845625/SRX8845625.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:22:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845625/SRX8845625.20_summits.bed INFO @ Thu, 09 Dec 2021 00:22:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2580 records, 4 fields): 4 millis CompletedMACS2peakCalling