Job ID = 14158237 SRX = SRX10641212 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: 00:24:58 19461580 reads; of these: 19461580 (100.00%) were paired; of these: 12159288 (62.48%) aligned concordantly 0 times 6269714 (32.22%) aligned concordantly exactly 1 time 1032578 (5.31%) aligned concordantly >1 times ---- 12159288 pairs aligned concordantly 0 times; of these: 2658725 (21.87%) aligned discordantly 1 time ---- 9500563 pairs aligned 0 times concordantly or discordantly; of these: 19001126 mates make up the pairs; of these: 17770841 (93.53%) aligned 0 times 682431 (3.59%) aligned exactly 1 time 547854 (2.88%) aligned >1 times 54.34% overall alignment rate Time searching: 00:24:58 Overall time: 00:24:58 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] 1464965 / 9924601 = 0.1476 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 15:35:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641212/SRX10641212.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641212/SRX10641212.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641212/SRX10641212.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641212/SRX10641212.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 15:35:42: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:35:42: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:35:50: 1000000 INFO @ Wed, 08 Dec 2021 15:35:57: 2000000 INFO @ Wed, 08 Dec 2021 15:36:04: 3000000 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 15:36:11: 4000000 INFO @ Wed, 08 Dec 2021 15:36:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641212/SRX10641212.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641212/SRX10641212.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641212/SRX10641212.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641212/SRX10641212.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 15:36:12: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:36:12: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:36:18: 5000000 INFO @ Wed, 08 Dec 2021 15:36:20: 1000000 INFO @ Wed, 08 Dec 2021 15:36:26: 6000000 INFO @ Wed, 08 Dec 2021 15:36:27: 2000000 INFO @ Wed, 08 Dec 2021 15:36:34: 7000000 INFO @ Wed, 08 Dec 2021 15:36:34: 3000000 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 15:36:42: 8000000 INFO @ Wed, 08 Dec 2021 15:36:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641212/SRX10641212.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641212/SRX10641212.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641212/SRX10641212.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641212/SRX10641212.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 15:36:42: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:36:42: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:36:43: 4000000 INFO @ Wed, 08 Dec 2021 15:36:51: 9000000 INFO @ Wed, 08 Dec 2021 15:36:51: 1000000 INFO @ Wed, 08 Dec 2021 15:36:51: 5000000 INFO @ Wed, 08 Dec 2021 15:36:58: 2000000 INFO @ Wed, 08 Dec 2021 15:36:59: 10000000 INFO @ Wed, 08 Dec 2021 15:37:00: 6000000 INFO @ Wed, 08 Dec 2021 15:37:06: 3000000 INFO @ Wed, 08 Dec 2021 15:37:08: 11000000 INFO @ Wed, 08 Dec 2021 15:37:08: 7000000 INFO @ Wed, 08 Dec 2021 15:37:13: 4000000 INFO @ Wed, 08 Dec 2021 15:37:16: 12000000 INFO @ Wed, 08 Dec 2021 15:37:17: 8000000 INFO @ Wed, 08 Dec 2021 15:37:21: 5000000 INFO @ Wed, 08 Dec 2021 15:37:24: 13000000 INFO @ Wed, 08 Dec 2021 15:37:24: 9000000 INFO @ Wed, 08 Dec 2021 15:37:28: 6000000 INFO @ Wed, 08 Dec 2021 15:37:32: 14000000 INFO @ Wed, 08 Dec 2021 15:37:32: 10000000 INFO @ Wed, 08 Dec 2021 15:37:36: 7000000 INFO @ Wed, 08 Dec 2021 15:37:39: 11000000 INFO @ Wed, 08 Dec 2021 15:37:39: 15000000 INFO @ Wed, 08 Dec 2021 15:37:43: 8000000 INFO @ Wed, 08 Dec 2021 15:37:47: 12000000 INFO @ Wed, 08 Dec 2021 15:37:48: 16000000 INFO @ Wed, 08 Dec 2021 15:37:50: 9000000 INFO @ Wed, 08 Dec 2021 15:37:54: 13000000 INFO @ Wed, 08 Dec 2021 15:37:56: 17000000 INFO @ Wed, 08 Dec 2021 15:37:57: 10000000 INFO @ Wed, 08 Dec 2021 15:38:01: 14000000 INFO @ Wed, 08 Dec 2021 15:38:04: 18000000 INFO @ Wed, 08 Dec 2021 15:38:05: 11000000 INFO @ Wed, 08 Dec 2021 15:38:05: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 15:38:05: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 15:38:05: #1 total tags in treatment: 6152270 INFO @ Wed, 08 Dec 2021 15:38:05: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:38:05: #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 15:38:05: #1 tags after filtering in treatment: 5705335 INFO @ Wed, 08 Dec 2021 15:38:05: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 15:38:05: #1 finished! INFO @ Wed, 08 Dec 2021 15:38:05: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:38:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:38:06: #2 number of paired peaks: 530 WARNING @ Wed, 08 Dec 2021 15:38:06: Fewer paired peaks (530) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 530 pairs to build model! INFO @ Wed, 08 Dec 2021 15:38:06: start model_add_line... INFO @ Wed, 08 Dec 2021 15:38:06: start X-correlation... INFO @ Wed, 08 Dec 2021 15:38:06: end of X-cor INFO @ Wed, 08 Dec 2021 15:38:06: #2 finished! INFO @ Wed, 08 Dec 2021 15:38:06: #2 predicted fragment length is 223 bps INFO @ Wed, 08 Dec 2021 15:38:06: #2 alternative fragment length(s) may be 223 bps INFO @ Wed, 08 Dec 2021 15:38:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641212/SRX10641212.05_model.r WARNING @ Wed, 08 Dec 2021 15:38:06: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 15:38:06: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Wed, 08 Dec 2021 15:38:06: #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 15:38:06: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:38:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:38:09: 15000000 INFO @ Wed, 08 Dec 2021 15:38:12: 12000000 INFO @ Wed, 08 Dec 2021 15:38:16: 16000000 INFO @ Wed, 08 Dec 2021 15:38:19: 13000000 INFO @ Wed, 08 Dec 2021 15:38:20: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 15:38:24: 17000000 INFO @ Wed, 08 Dec 2021 15:38:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641212/SRX10641212.05_peaks.xls INFO @ Wed, 08 Dec 2021 15:38:27: 14000000 INFO @ Wed, 08 Dec 2021 15:38:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641212/SRX10641212.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:38:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641212/SRX10641212.05_summits.bed INFO @ Wed, 08 Dec 2021 15:38:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (437 records, 4 fields): 61 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 15:38:32: 18000000 INFO @ Wed, 08 Dec 2021 15:38:33: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 15:38:33: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 15:38:33: #1 total tags in treatment: 6152270 INFO @ Wed, 08 Dec 2021 15:38:33: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:38:33: #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 15:38:34: #1 tags after filtering in treatment: 5705335 INFO @ Wed, 08 Dec 2021 15:38:34: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 15:38:34: #1 finished! INFO @ Wed, 08 Dec 2021 15:38:34: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:38:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:38:34: #2 number of paired peaks: 530 WARNING @ Wed, 08 Dec 2021 15:38:34: Fewer paired peaks (530) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 530 pairs to build model! INFO @ Wed, 08 Dec 2021 15:38:34: start model_add_line... INFO @ Wed, 08 Dec 2021 15:38:34: start X-correlation... INFO @ Wed, 08 Dec 2021 15:38:34: end of X-cor INFO @ Wed, 08 Dec 2021 15:38:34: #2 finished! INFO @ Wed, 08 Dec 2021 15:38:34: #2 predicted fragment length is 223 bps INFO @ Wed, 08 Dec 2021 15:38:34: #2 alternative fragment length(s) may be 223 bps INFO @ Wed, 08 Dec 2021 15:38:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641212/SRX10641212.10_model.r WARNING @ Wed, 08 Dec 2021 15:38:34: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 15:38:34: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Wed, 08 Dec 2021 15:38:34: #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 15:38:34: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:38:34: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:38:35: 15000000 INFO @ Wed, 08 Dec 2021 15:38:42: 16000000 INFO @ Wed, 08 Dec 2021 15:38:48: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:38:49: 17000000 INFO @ Wed, 08 Dec 2021 15:38:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641212/SRX10641212.10_peaks.xls INFO @ Wed, 08 Dec 2021 15:38:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641212/SRX10641212.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:38:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641212/SRX10641212.10_summits.bed INFO @ Wed, 08 Dec 2021 15:38:54: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (317 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 15:38:56: 18000000 INFO @ Wed, 08 Dec 2021 15:38:57: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 15:38:57: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 15:38:57: #1 total tags in treatment: 6152270 INFO @ Wed, 08 Dec 2021 15:38:57: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:38:57: #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 15:38:58: #1 tags after filtering in treatment: 5705335 INFO @ Wed, 08 Dec 2021 15:38:58: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 15:38:58: #1 finished! INFO @ Wed, 08 Dec 2021 15:38:58: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:38:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:38:58: #2 number of paired peaks: 530 WARNING @ Wed, 08 Dec 2021 15:38:58: Fewer paired peaks (530) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 530 pairs to build model! INFO @ Wed, 08 Dec 2021 15:38:58: start model_add_line... INFO @ Wed, 08 Dec 2021 15:38:58: start X-correlation... INFO @ Wed, 08 Dec 2021 15:38:58: end of X-cor INFO @ Wed, 08 Dec 2021 15:38:58: #2 finished! INFO @ Wed, 08 Dec 2021 15:38:58: #2 predicted fragment length is 223 bps INFO @ Wed, 08 Dec 2021 15:38:58: #2 alternative fragment length(s) may be 223 bps INFO @ Wed, 08 Dec 2021 15:38:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641212/SRX10641212.20_model.r WARNING @ Wed, 08 Dec 2021 15:38:58: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 15:38:58: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Wed, 08 Dec 2021 15:38:58: #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 15:38:58: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:38:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 15:39:11: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:39:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641212/SRX10641212.20_peaks.xls INFO @ Wed, 08 Dec 2021 15:39:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641212/SRX10641212.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:39:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641212/SRX10641212.20_summits.bed INFO @ Wed, 08 Dec 2021 15:39:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (228 records, 4 fields): 1 millis CompletedMACS2peakCalling