Job ID = 14160611 SRX = SRX9567173 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: 01:30:21 20321940 reads; of these: 20321940 (100.00%) were paired; of these: 7513539 (36.97%) aligned concordantly 0 times 6662383 (32.78%) aligned concordantly exactly 1 time 6146018 (30.24%) aligned concordantly >1 times ---- 7513539 pairs aligned concordantly 0 times; of these: 5159305 (68.67%) aligned discordantly 1 time ---- 2354234 pairs aligned 0 times concordantly or discordantly; of these: 4708468 mates make up the pairs; of these: 1940907 (41.22%) aligned 0 times 1238426 (26.30%) aligned exactly 1 time 1529135 (32.48%) aligned >1 times 95.22% overall alignment rate Time searching: 01:30:21 Overall time: 01:30:21 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 32 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] 12452537 / 17942898 = 0.6940 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 05:10:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9567173/SRX9567173.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9567173/SRX9567173.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9567173/SRX9567173.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9567173/SRX9567173.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 05:10:40: #1 read tag files... INFO @ Thu, 09 Dec 2021 05:10:40: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 05:10:52: 1000000 INFO @ Thu, 09 Dec 2021 05:11:04: 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 @ Thu, 09 Dec 2021 05:11:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9567173/SRX9567173.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9567173/SRX9567173.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9567173/SRX9567173.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9567173/SRX9567173.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 05:11:10: #1 read tag files... INFO @ Thu, 09 Dec 2021 05:11:10: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 05:11:17: 3000000 INFO @ Thu, 09 Dec 2021 05:11:25: 1000000 INFO @ Thu, 09 Dec 2021 05:11:29: 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 05:11:39: 2000000 INFO @ Thu, 09 Dec 2021 05:11:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9567173/SRX9567173.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9567173/SRX9567173.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9567173/SRX9567173.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9567173/SRX9567173.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 05:11:40: #1 read tag files... INFO @ Thu, 09 Dec 2021 05:11:40: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 05:11:41: 5000000 INFO @ Thu, 09 Dec 2021 05:11:52: 1000000 INFO @ Thu, 09 Dec 2021 05:11:54: 3000000 INFO @ Thu, 09 Dec 2021 05:11:54: 6000000 INFO @ Thu, 09 Dec 2021 05:12:03: 2000000 INFO @ Thu, 09 Dec 2021 05:12:07: 7000000 INFO @ Thu, 09 Dec 2021 05:12:09: 4000000 INFO @ Thu, 09 Dec 2021 05:12:15: 3000000 INFO @ Thu, 09 Dec 2021 05:12:19: 8000000 INFO @ Thu, 09 Dec 2021 05:12:23: 5000000 INFO @ Thu, 09 Dec 2021 05:12:26: 4000000 INFO @ Thu, 09 Dec 2021 05:12:32: 9000000 INFO @ Thu, 09 Dec 2021 05:12:38: 5000000 INFO @ Thu, 09 Dec 2021 05:12:39: 6000000 INFO @ Thu, 09 Dec 2021 05:12:44: 10000000 INFO @ Thu, 09 Dec 2021 05:12:49: 6000000 INFO @ Thu, 09 Dec 2021 05:12:54: 7000000 INFO @ Thu, 09 Dec 2021 05:12:57: 11000000 INFO @ Thu, 09 Dec 2021 05:13:01: 7000000 INFO @ Thu, 09 Dec 2021 05:13:09: 8000000 INFO @ Thu, 09 Dec 2021 05:13:09: 12000000 INFO @ Thu, 09 Dec 2021 05:13:12: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 05:13:20: 13000000 INFO @ Thu, 09 Dec 2021 05:13:23: 9000000 INFO @ Thu, 09 Dec 2021 05:13:24: 9000000 INFO @ Thu, 09 Dec 2021 05:13:29: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 05:13:29: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 05:13:29: #1 total tags in treatment: 3933017 INFO @ Thu, 09 Dec 2021 05:13:29: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 05:13:29: #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 05:13:29: #1 tags after filtering in treatment: 2525233 INFO @ Thu, 09 Dec 2021 05:13:29: #1 Redundant rate of treatment: 0.36 INFO @ Thu, 09 Dec 2021 05:13:29: #1 finished! INFO @ Thu, 09 Dec 2021 05:13:29: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 05:13:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 05:13:29: #2 number of paired peaks: 1115 INFO @ Thu, 09 Dec 2021 05:13:29: start model_add_line... INFO @ Thu, 09 Dec 2021 05:13:29: start X-correlation... INFO @ Thu, 09 Dec 2021 05:13:30: end of X-cor INFO @ Thu, 09 Dec 2021 05:13:30: #2 finished! INFO @ Thu, 09 Dec 2021 05:13:30: #2 predicted fragment length is 302 bps INFO @ Thu, 09 Dec 2021 05:13:30: #2 alternative fragment length(s) may be 302 bps INFO @ Thu, 09 Dec 2021 05:13:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9567173/SRX9567173.05_model.r WARNING @ Thu, 09 Dec 2021 05:13:30: #2 Since the d (302) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 05:13:30: #2 You may need to consider one of the other alternative d(s): 302 WARNING @ Thu, 09 Dec 2021 05:13:30: #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 05:13:30: #3 Call peaks... INFO @ Thu, 09 Dec 2021 05:13:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 05:13:36: 10000000 INFO @ Thu, 09 Dec 2021 05:13:38: 10000000 INFO @ Thu, 09 Dec 2021 05:13:41: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 05:13:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9567173/SRX9567173.05_peaks.xls INFO @ Thu, 09 Dec 2021 05:13:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9567173/SRX9567173.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 05:13:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9567173/SRX9567173.05_summits.bed INFO @ Thu, 09 Dec 2021 05:13:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (751 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 05:13:46: 11000000 INFO @ Thu, 09 Dec 2021 05:13:52: 11000000 INFO @ Thu, 09 Dec 2021 05:13:57: 12000000 INFO @ Thu, 09 Dec 2021 05:14:05: 12000000 INFO @ Thu, 09 Dec 2021 05:14:08: 13000000 INFO @ Thu, 09 Dec 2021 05:14:16: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 05:14:16: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 05:14:16: #1 total tags in treatment: 3933017 INFO @ Thu, 09 Dec 2021 05:14:16: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 05:14:16: #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 05:14:16: #1 tags after filtering in treatment: 2525233 INFO @ Thu, 09 Dec 2021 05:14:16: #1 Redundant rate of treatment: 0.36 INFO @ Thu, 09 Dec 2021 05:14:16: #1 finished! INFO @ Thu, 09 Dec 2021 05:14:16: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 05:14:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 05:14:17: #2 number of paired peaks: 1115 INFO @ Thu, 09 Dec 2021 05:14:17: start model_add_line... INFO @ Thu, 09 Dec 2021 05:14:17: start X-correlation... INFO @ Thu, 09 Dec 2021 05:14:17: end of X-cor INFO @ Thu, 09 Dec 2021 05:14:17: #2 finished! INFO @ Thu, 09 Dec 2021 05:14:17: #2 predicted fragment length is 302 bps INFO @ Thu, 09 Dec 2021 05:14:17: #2 alternative fragment length(s) may be 302 bps INFO @ Thu, 09 Dec 2021 05:14:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9567173/SRX9567173.20_model.r WARNING @ Thu, 09 Dec 2021 05:14:17: #2 Since the d (302) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 05:14:17: #2 You may need to consider one of the other alternative d(s): 302 WARNING @ Thu, 09 Dec 2021 05:14:17: #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 05:14:17: #3 Call peaks... INFO @ Thu, 09 Dec 2021 05:14:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 05:14:18: 13000000 INFO @ Thu, 09 Dec 2021 05:14:28: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 05:14:28: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 05:14:28: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 05:14:28: #1 total tags in treatment: 3933017 INFO @ Thu, 09 Dec 2021 05:14:28: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 05:14:28: #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 05:14:28: #1 tags after filtering in treatment: 2525233 INFO @ Thu, 09 Dec 2021 05:14:28: #1 Redundant rate of treatment: 0.36 INFO @ Thu, 09 Dec 2021 05:14:28: #1 finished! INFO @ Thu, 09 Dec 2021 05:14:28: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 05:14:28: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 05:14:29: #2 number of paired peaks: 1115 INFO @ Thu, 09 Dec 2021 05:14:29: start model_add_line... INFO @ Thu, 09 Dec 2021 05:14:29: start X-correlation... INFO @ Thu, 09 Dec 2021 05:14:29: end of X-cor INFO @ Thu, 09 Dec 2021 05:14:29: #2 finished! INFO @ Thu, 09 Dec 2021 05:14:29: #2 predicted fragment length is 302 bps INFO @ Thu, 09 Dec 2021 05:14:29: #2 alternative fragment length(s) may be 302 bps INFO @ Thu, 09 Dec 2021 05:14:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9567173/SRX9567173.10_model.r WARNING @ Thu, 09 Dec 2021 05:14:29: #2 Since the d (302) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 05:14:29: #2 You may need to consider one of the other alternative d(s): 302 WARNING @ Thu, 09 Dec 2021 05:14:29: #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 05:14:29: #3 Call peaks... INFO @ Thu, 09 Dec 2021 05:14:29: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 05:14:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9567173/SRX9567173.20_peaks.xls INFO @ Thu, 09 Dec 2021 05:14:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9567173/SRX9567173.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 05:14:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9567173/SRX9567173.20_summits.bed INFO @ Thu, 09 Dec 2021 05:14:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (460 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 05:14:40: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 05:14:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9567173/SRX9567173.10_peaks.xls INFO @ Thu, 09 Dec 2021 05:14:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9567173/SRX9567173.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 05:14:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9567173/SRX9567173.10_summits.bed INFO @ Thu, 09 Dec 2021 05:14:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (593 records, 4 fields): 4 millis CompletedMACS2peakCalling