Job ID = 14159278 SRX = SRX10641189 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:33:04 25050789 reads; of these: 25050789 (100.00%) were paired; of these: 18353714 (73.27%) aligned concordantly 0 times 5878348 (23.47%) aligned concordantly exactly 1 time 818727 (3.27%) aligned concordantly >1 times ---- 18353714 pairs aligned concordantly 0 times; of these: 2820289 (15.37%) aligned discordantly 1 time ---- 15533425 pairs aligned 0 times concordantly or discordantly; of these: 31066850 mates make up the pairs; of these: 29681124 (95.54%) aligned 0 times 755570 (2.43%) aligned exactly 1 time 630156 (2.03%) aligned >1 times 40.76% overall alignment rate Time searching: 00:33:05 Overall time: 00:33:05 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 16 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] 1399138 / 9492085 = 0.1474 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 21:22:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641189/SRX10641189.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641189/SRX10641189.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641189/SRX10641189.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641189/SRX10641189.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 21:22:55: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:22:55: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:23:08: 1000000 INFO @ Wed, 08 Dec 2021 21:23:21: 2000000 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 21:23:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641189/SRX10641189.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641189/SRX10641189.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641189/SRX10641189.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641189/SRX10641189.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 21:23:24: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:23:24: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:23:35: 3000000 INFO @ Wed, 08 Dec 2021 21:23:40: 1000000 INFO @ Wed, 08 Dec 2021 21:23:49: 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 21:23:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641189/SRX10641189.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641189/SRX10641189.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641189/SRX10641189.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641189/SRX10641189.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 21:23:54: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:23:54: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:23:55: 2000000 INFO @ Wed, 08 Dec 2021 21:24:02: 5000000 INFO @ Wed, 08 Dec 2021 21:24:09: 1000000 INFO @ Wed, 08 Dec 2021 21:24:12: 3000000 INFO @ Wed, 08 Dec 2021 21:24:16: 6000000 INFO @ Wed, 08 Dec 2021 21:24:23: 2000000 INFO @ Wed, 08 Dec 2021 21:24:28: 4000000 INFO @ Wed, 08 Dec 2021 21:24:31: 7000000 INFO @ Wed, 08 Dec 2021 21:24:37: 3000000 INFO @ Wed, 08 Dec 2021 21:24:44: 8000000 INFO @ Wed, 08 Dec 2021 21:24:44: 5000000 INFO @ Wed, 08 Dec 2021 21:24:51: 4000000 INFO @ Wed, 08 Dec 2021 21:24:59: 9000000 INFO @ Wed, 08 Dec 2021 21:25:01: 6000000 INFO @ Wed, 08 Dec 2021 21:25:05: 5000000 INFO @ Wed, 08 Dec 2021 21:25:12: 10000000 INFO @ Wed, 08 Dec 2021 21:25:17: 7000000 INFO @ Wed, 08 Dec 2021 21:25:21: 6000000 INFO @ Wed, 08 Dec 2021 21:25:26: 11000000 INFO @ Wed, 08 Dec 2021 21:25:33: 8000000 INFO @ Wed, 08 Dec 2021 21:25:36: 7000000 INFO @ Wed, 08 Dec 2021 21:25:39: 12000000 INFO @ Wed, 08 Dec 2021 21:25:49: 9000000 INFO @ Wed, 08 Dec 2021 21:25:51: 8000000 INFO @ Wed, 08 Dec 2021 21:25:53: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 21:26:06: 9000000 INFO @ Wed, 08 Dec 2021 21:26:06: 10000000 INFO @ Wed, 08 Dec 2021 21:26:07: 14000000 INFO @ Wed, 08 Dec 2021 21:26:20: 10000000 INFO @ Wed, 08 Dec 2021 21:26:21: 15000000 INFO @ Wed, 08 Dec 2021 21:26:22: 11000000 INFO @ Wed, 08 Dec 2021 21:26:34: 11000000 INFO @ Wed, 08 Dec 2021 21:26:35: 16000000 INFO @ Wed, 08 Dec 2021 21:26:38: 12000000 INFO @ Wed, 08 Dec 2021 21:26:48: 12000000 INFO @ Wed, 08 Dec 2021 21:26:49: 17000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 21:26:55: 13000000 INFO @ Wed, 08 Dec 2021 21:26:58: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 21:26:58: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 21:26:58: #1 total tags in treatment: 5629231 INFO @ Wed, 08 Dec 2021 21:26:58: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:26:58: #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 21:26:58: #1 tags after filtering in treatment: 5194178 INFO @ Wed, 08 Dec 2021 21:26:58: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 21:26:58: #1 finished! INFO @ Wed, 08 Dec 2021 21:26:58: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:26:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:26:58: #2 number of paired peaks: 1685 INFO @ Wed, 08 Dec 2021 21:26:58: start model_add_line... INFO @ Wed, 08 Dec 2021 21:26:58: start X-correlation... INFO @ Wed, 08 Dec 2021 21:26:58: end of X-cor INFO @ Wed, 08 Dec 2021 21:26:58: #2 finished! INFO @ Wed, 08 Dec 2021 21:26:58: #2 predicted fragment length is 252 bps INFO @ Wed, 08 Dec 2021 21:26:58: #2 alternative fragment length(s) may be 4,252 bps INFO @ Wed, 08 Dec 2021 21:26:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641189/SRX10641189.05_model.r WARNING @ Wed, 08 Dec 2021 21:26:58: #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 21:26:58: #2 You may need to consider one of the other alternative d(s): 4,252 WARNING @ Wed, 08 Dec 2021 21:26:58: #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 21:26:58: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:26:58: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:27:02: 13000000 INFO @ Wed, 08 Dec 2021 21:27:12: 14000000 INFO @ Wed, 08 Dec 2021 21:27:16: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:27:17: 14000000 INFO @ Wed, 08 Dec 2021 21:27:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641189/SRX10641189.05_peaks.xls INFO @ Wed, 08 Dec 2021 21:27:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641189/SRX10641189.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:27:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641189/SRX10641189.05_summits.bed INFO @ Wed, 08 Dec 2021 21:27:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1656 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:27:29: 15000000 INFO @ Wed, 08 Dec 2021 21:27:31: 15000000 INFO @ Wed, 08 Dec 2021 21:27:45: 16000000 INFO @ Wed, 08 Dec 2021 21:27:46: 16000000 INFO @ Wed, 08 Dec 2021 21:28:00: 17000000 INFO @ Wed, 08 Dec 2021 21:28:03: 17000000 INFO @ Wed, 08 Dec 2021 21:28:09: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 21:28:09: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 21:28:09: #1 total tags in treatment: 5629231 INFO @ Wed, 08 Dec 2021 21:28:09: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:28:09: #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 21:28:09: #1 tags after filtering in treatment: 5194178 INFO @ Wed, 08 Dec 2021 21:28:09: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 21:28:09: #1 finished! INFO @ Wed, 08 Dec 2021 21:28:09: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:28:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:28:10: #2 number of paired peaks: 1685 INFO @ Wed, 08 Dec 2021 21:28:10: start model_add_line... INFO @ Wed, 08 Dec 2021 21:28:10: start X-correlation... INFO @ Wed, 08 Dec 2021 21:28:10: end of X-cor INFO @ Wed, 08 Dec 2021 21:28:10: #2 finished! INFO @ Wed, 08 Dec 2021 21:28:10: #2 predicted fragment length is 252 bps INFO @ Wed, 08 Dec 2021 21:28:10: #2 alternative fragment length(s) may be 4,252 bps INFO @ Wed, 08 Dec 2021 21:28:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641189/SRX10641189.20_model.r WARNING @ Wed, 08 Dec 2021 21:28:10: #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 21:28:10: #2 You may need to consider one of the other alternative d(s): 4,252 WARNING @ Wed, 08 Dec 2021 21:28:10: #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 21:28:10: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:28:10: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:28:13: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 21:28:13: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 21:28:13: #1 total tags in treatment: 5629231 INFO @ Wed, 08 Dec 2021 21:28:13: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:28:13: #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 21:28:13: #1 tags after filtering in treatment: 5194178 INFO @ Wed, 08 Dec 2021 21:28:13: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 21:28:13: #1 finished! INFO @ Wed, 08 Dec 2021 21:28:13: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:28:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:28:14: #2 number of paired peaks: 1685 INFO @ Wed, 08 Dec 2021 21:28:14: start model_add_line... INFO @ Wed, 08 Dec 2021 21:28:14: start X-correlation... INFO @ Wed, 08 Dec 2021 21:28:14: end of X-cor INFO @ Wed, 08 Dec 2021 21:28:14: #2 finished! INFO @ Wed, 08 Dec 2021 21:28:14: #2 predicted fragment length is 252 bps INFO @ Wed, 08 Dec 2021 21:28:14: #2 alternative fragment length(s) may be 4,252 bps INFO @ Wed, 08 Dec 2021 21:28:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641189/SRX10641189.10_model.r WARNING @ Wed, 08 Dec 2021 21:28:14: #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 21:28:14: #2 You may need to consider one of the other alternative d(s): 4,252 WARNING @ Wed, 08 Dec 2021 21:28:14: #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 21:28:14: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:28:14: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:28:27: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:28:31: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:28:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641189/SRX10641189.20_peaks.xls INFO @ Wed, 08 Dec 2021 21:28:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641189/SRX10641189.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:28:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641189/SRX10641189.20_summits.bed INFO @ Wed, 08 Dec 2021 21:28:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (396 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:28:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641189/SRX10641189.10_peaks.xls INFO @ Wed, 08 Dec 2021 21:28:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641189/SRX10641189.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:28:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641189/SRX10641189.10_summits.bed INFO @ Wed, 08 Dec 2021 21:28:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (768 records, 4 fields): 104 millis CompletedMACS2peakCalling