Job ID = 14158307 SRX = SRX10641213 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: 00:21:15 15590980 reads; of these: 15590980 (100.00%) were paired; of these: 9433965 (60.51%) aligned concordantly 0 times 5104595 (32.74%) aligned concordantly exactly 1 time 1052420 (6.75%) aligned concordantly >1 times ---- 9433965 pairs aligned concordantly 0 times; of these: 2523968 (26.75%) aligned discordantly 1 time ---- 6909997 pairs aligned 0 times concordantly or discordantly; of these: 13819994 mates make up the pairs; of these: 12628581 (91.38%) aligned 0 times 647096 (4.68%) aligned exactly 1 time 544317 (3.94%) aligned >1 times 59.50% overall alignment rate Time searching: 00:21:16 Overall time: 00:21:16 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] 1180998 / 8638760 = 0.1367 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 16:23:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641213/SRX10641213.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641213/SRX10641213.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641213/SRX10641213.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641213/SRX10641213.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 16:23:08: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:23:08: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:23:16: 1000000 INFO @ Wed, 08 Dec 2021 16:23:25: 2000000 INFO @ Wed, 08 Dec 2021 16:23:33: 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 16:23:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641213/SRX10641213.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641213/SRX10641213.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641213/SRX10641213.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641213/SRX10641213.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 16:23:38: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:23:38: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:23:42: 4000000 INFO @ Wed, 08 Dec 2021 16:23:49: 1000000 INFO @ Wed, 08 Dec 2021 16:23:53: 5000000 INFO @ Wed, 08 Dec 2021 16:24:00: 2000000 INFO @ Wed, 08 Dec 2021 16:24:04: 6000000 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 16:24:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641213/SRX10641213.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641213/SRX10641213.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641213/SRX10641213.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641213/SRX10641213.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 16:24:08: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:24:08: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:24:11: 3000000 INFO @ Wed, 08 Dec 2021 16:24:15: 7000000 INFO @ Wed, 08 Dec 2021 16:24:18: 1000000 INFO @ Wed, 08 Dec 2021 16:24:22: 4000000 INFO @ Wed, 08 Dec 2021 16:24:27: 8000000 INFO @ Wed, 08 Dec 2021 16:24:27: 2000000 INFO @ Wed, 08 Dec 2021 16:24:33: 5000000 INFO @ Wed, 08 Dec 2021 16:24:37: 3000000 INFO @ Wed, 08 Dec 2021 16:24:37: 9000000 INFO @ Wed, 08 Dec 2021 16:24:44: 6000000 INFO @ Wed, 08 Dec 2021 16:24:47: 4000000 INFO @ Wed, 08 Dec 2021 16:24:48: 10000000 INFO @ Wed, 08 Dec 2021 16:24:55: 7000000 INFO @ Wed, 08 Dec 2021 16:24:57: 5000000 INFO @ Wed, 08 Dec 2021 16:24:58: 11000000 INFO @ Wed, 08 Dec 2021 16:25:06: 8000000 INFO @ Wed, 08 Dec 2021 16:25:06: 6000000 INFO @ Wed, 08 Dec 2021 16:25:08: 12000000 INFO @ Wed, 08 Dec 2021 16:25:16: 7000000 INFO @ Wed, 08 Dec 2021 16:25:17: 9000000 INFO @ Wed, 08 Dec 2021 16:25:18: 13000000 INFO @ Wed, 08 Dec 2021 16:25:26: 8000000 INFO @ Wed, 08 Dec 2021 16:25:28: 10000000 INFO @ Wed, 08 Dec 2021 16:25:28: 14000000 INFO @ Wed, 08 Dec 2021 16:25:36: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 16:25:39: 15000000 INFO @ Wed, 08 Dec 2021 16:25:39: 11000000 INFO @ Wed, 08 Dec 2021 16:25:46: 10000000 INFO @ Wed, 08 Dec 2021 16:25:49: 16000000 INFO @ Wed, 08 Dec 2021 16:25:50: 12000000 INFO @ Wed, 08 Dec 2021 16:25:51: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 16:25:51: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 16:25:51: #1 total tags in treatment: 5249326 INFO @ Wed, 08 Dec 2021 16:25:51: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:25:51: #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 16:25:51: #1 tags after filtering in treatment: 4785990 INFO @ Wed, 08 Dec 2021 16:25:51: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 08 Dec 2021 16:25:51: #1 finished! INFO @ Wed, 08 Dec 2021 16:25:51: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:25:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:25:52: #2 number of paired peaks: 610 WARNING @ Wed, 08 Dec 2021 16:25:52: Fewer paired peaks (610) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 610 pairs to build model! INFO @ Wed, 08 Dec 2021 16:25:52: start model_add_line... INFO @ Wed, 08 Dec 2021 16:25:52: start X-correlation... INFO @ Wed, 08 Dec 2021 16:25:52: end of X-cor INFO @ Wed, 08 Dec 2021 16:25:52: #2 finished! INFO @ Wed, 08 Dec 2021 16:25:52: #2 predicted fragment length is 216 bps INFO @ Wed, 08 Dec 2021 16:25:52: #2 alternative fragment length(s) may be 216 bps INFO @ Wed, 08 Dec 2021 16:25:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641213/SRX10641213.05_model.r INFO @ Wed, 08 Dec 2021 16:25:56: 11000000 INFO @ Wed, 08 Dec 2021 16:26:00: 13000000 WARNING @ Wed, 08 Dec 2021 16:26:04: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 16:26:04: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Wed, 08 Dec 2021 16:26:04: #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 16:26:04: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:26:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:26:05: 12000000 INFO @ Wed, 08 Dec 2021 16:26:11: 14000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 16:26:15: 13000000 INFO @ Wed, 08 Dec 2021 16:26:16: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:26:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641213/SRX10641213.05_peaks.xls INFO @ Wed, 08 Dec 2021 16:26:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641213/SRX10641213.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:26:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641213/SRX10641213.05_summits.bed INFO @ Wed, 08 Dec 2021 16:26:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (407 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 16:26:22: 15000000 INFO @ Wed, 08 Dec 2021 16:26:25: 14000000 INFO @ Wed, 08 Dec 2021 16:26:33: 16000000 INFO @ Wed, 08 Dec 2021 16:26:35: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 16:26:35: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 16:26:35: #1 total tags in treatment: 5249326 INFO @ Wed, 08 Dec 2021 16:26:35: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:26:35: #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 16:26:35: #1 tags after filtering in treatment: 4785990 INFO @ Wed, 08 Dec 2021 16:26:35: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 08 Dec 2021 16:26:35: #1 finished! INFO @ Wed, 08 Dec 2021 16:26:35: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:26:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:26:35: 15000000 INFO @ Wed, 08 Dec 2021 16:26:35: #2 number of paired peaks: 610 WARNING @ Wed, 08 Dec 2021 16:26:35: Fewer paired peaks (610) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 610 pairs to build model! INFO @ Wed, 08 Dec 2021 16:26:35: start model_add_line... INFO @ Wed, 08 Dec 2021 16:26:35: start X-correlation... INFO @ Wed, 08 Dec 2021 16:26:35: end of X-cor INFO @ Wed, 08 Dec 2021 16:26:35: #2 finished! INFO @ Wed, 08 Dec 2021 16:26:35: #2 predicted fragment length is 216 bps INFO @ Wed, 08 Dec 2021 16:26:35: #2 alternative fragment length(s) may be 216 bps INFO @ Wed, 08 Dec 2021 16:26:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641213/SRX10641213.10_model.r WARNING @ Wed, 08 Dec 2021 16:26:35: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 16:26:35: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Wed, 08 Dec 2021 16:26:35: #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 16:26:35: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:26:35: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:26:43: 16000000 INFO @ Wed, 08 Dec 2021 16:26:45: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 16:26:45: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 16:26:45: #1 total tags in treatment: 5249326 INFO @ Wed, 08 Dec 2021 16:26:45: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:26:45: #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 16:26:45: #1 tags after filtering in treatment: 4785990 INFO @ Wed, 08 Dec 2021 16:26:45: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 08 Dec 2021 16:26:45: #1 finished! INFO @ Wed, 08 Dec 2021 16:26:45: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:26:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:26:46: #2 number of paired peaks: 610 WARNING @ Wed, 08 Dec 2021 16:26:46: Fewer paired peaks (610) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 610 pairs to build model! INFO @ Wed, 08 Dec 2021 16:26:46: start model_add_line... INFO @ Wed, 08 Dec 2021 16:26:46: start X-correlation... INFO @ Wed, 08 Dec 2021 16:26:46: end of X-cor INFO @ Wed, 08 Dec 2021 16:26:46: #2 finished! INFO @ Wed, 08 Dec 2021 16:26:46: #2 predicted fragment length is 216 bps INFO @ Wed, 08 Dec 2021 16:26:46: #2 alternative fragment length(s) may be 216 bps INFO @ Wed, 08 Dec 2021 16:26:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641213/SRX10641213.20_model.r WARNING @ Wed, 08 Dec 2021 16:26:46: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 16:26:46: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Wed, 08 Dec 2021 16:26:46: #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 16:26:46: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:26:46: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:26:47: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:26:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641213/SRX10641213.10_peaks.xls INFO @ Wed, 08 Dec 2021 16:26:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641213/SRX10641213.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:26:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641213/SRX10641213.10_summits.bed INFO @ Wed, 08 Dec 2021 16:26:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (324 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 16:26:57: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:27:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641213/SRX10641213.20_peaks.xls INFO @ Wed, 08 Dec 2021 16:27:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641213/SRX10641213.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:27:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641213/SRX10641213.20_summits.bed INFO @ Wed, 08 Dec 2021 16:27:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (227 records, 4 fields): 2 millis CompletedMACS2peakCalling