Job ID = 14158306 SRX = SRX10641216 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: 00:19:21 21779135 reads; of these: 21779135 (100.00%) were paired; of these: 16257604 (74.65%) aligned concordantly 0 times 4791426 (22.00%) aligned concordantly exactly 1 time 730105 (3.35%) aligned concordantly >1 times ---- 16257604 pairs aligned concordantly 0 times; of these: 2636962 (16.22%) aligned discordantly 1 time ---- 13620642 pairs aligned 0 times concordantly or discordantly; of these: 27241284 mates make up the pairs; of these: 25814520 (94.76%) aligned 0 times 825345 (3.03%) aligned exactly 1 time 601419 (2.21%) aligned >1 times 40.74% overall alignment rate Time searching: 00:19:21 Overall time: 00:19:21 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 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] 1330605 / 8134464 = 0.1636 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 16:20:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641216/SRX10641216.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641216/SRX10641216.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641216/SRX10641216.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641216/SRX10641216.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 16:20:15: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:20:15: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:20:24: 1000000 INFO @ Wed, 08 Dec 2021 16:20:34: 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 16:20:43: 3000000 INFO @ Wed, 08 Dec 2021 16:20:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641216/SRX10641216.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641216/SRX10641216.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641216/SRX10641216.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641216/SRX10641216.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 16:20:45: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:20:45: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:20:54: 4000000 INFO @ Wed, 08 Dec 2021 16:20:56: 1000000 INFO @ Wed, 08 Dec 2021 16:21:05: 5000000 INFO @ Wed, 08 Dec 2021 16:21:07: 2000000 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 16:21:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641216/SRX10641216.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641216/SRX10641216.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641216/SRX10641216.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641216/SRX10641216.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 16:21:15: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:21:15: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:21:16: 6000000 INFO @ Wed, 08 Dec 2021 16:21:18: 3000000 INFO @ Wed, 08 Dec 2021 16:21:26: 1000000 INFO @ Wed, 08 Dec 2021 16:21:27: 7000000 INFO @ Wed, 08 Dec 2021 16:21:29: 4000000 INFO @ Wed, 08 Dec 2021 16:21:37: 2000000 INFO @ Wed, 08 Dec 2021 16:21:38: 8000000 INFO @ Wed, 08 Dec 2021 16:21:40: 5000000 INFO @ Wed, 08 Dec 2021 16:21:48: 3000000 INFO @ Wed, 08 Dec 2021 16:21:49: 9000000 INFO @ Wed, 08 Dec 2021 16:21:51: 6000000 INFO @ Wed, 08 Dec 2021 16:22:00: 4000000 INFO @ Wed, 08 Dec 2021 16:22:01: 10000000 INFO @ Wed, 08 Dec 2021 16:22:03: 7000000 INFO @ Wed, 08 Dec 2021 16:22:11: 5000000 INFO @ Wed, 08 Dec 2021 16:22:12: 11000000 INFO @ Wed, 08 Dec 2021 16:22:14: 8000000 INFO @ Wed, 08 Dec 2021 16:22:22: 6000000 INFO @ Wed, 08 Dec 2021 16:22:23: 12000000 INFO @ Wed, 08 Dec 2021 16:22:25: 9000000 INFO @ Wed, 08 Dec 2021 16:22:34: 7000000 INFO @ Wed, 08 Dec 2021 16:22:34: 13000000 INFO @ Wed, 08 Dec 2021 16:22:36: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 16:22:45: 8000000 INFO @ Wed, 08 Dec 2021 16:22:46: 14000000 INFO @ Wed, 08 Dec 2021 16:22:48: 11000000 INFO @ Wed, 08 Dec 2021 16:22:56: 9000000 INFO @ Wed, 08 Dec 2021 16:22:57: 15000000 INFO @ Wed, 08 Dec 2021 16:22:58: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 16:22:58: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 16:22:58: #1 total tags in treatment: 4541633 INFO @ Wed, 08 Dec 2021 16:22:58: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:22:58: #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 16:22:58: #1 tags after filtering in treatment: 4245177 INFO @ Wed, 08 Dec 2021 16:22:58: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 16:22:58: #1 finished! INFO @ Wed, 08 Dec 2021 16:22:58: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:22:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:22:58: #2 number of paired peaks: 427 WARNING @ Wed, 08 Dec 2021 16:22:58: Fewer paired peaks (427) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 427 pairs to build model! INFO @ Wed, 08 Dec 2021 16:22:58: start model_add_line... INFO @ Wed, 08 Dec 2021 16:22:58: start X-correlation... INFO @ Wed, 08 Dec 2021 16:22:58: end of X-cor INFO @ Wed, 08 Dec 2021 16:22:58: #2 finished! INFO @ Wed, 08 Dec 2021 16:22:58: #2 predicted fragment length is 223 bps INFO @ Wed, 08 Dec 2021 16:22:58: #2 alternative fragment length(s) may be 223 bps INFO @ Wed, 08 Dec 2021 16:22:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641216/SRX10641216.05_model.r WARNING @ Wed, 08 Dec 2021 16:22:58: #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 16:22:58: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Wed, 08 Dec 2021 16:22:58: #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 16:22:58: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:22:58: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:22:59: 12000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 16:23:07: 10000000 INFO @ Wed, 08 Dec 2021 16:23:08: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:23:10: 13000000 INFO @ Wed, 08 Dec 2021 16:23:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641216/SRX10641216.05_peaks.xls INFO @ Wed, 08 Dec 2021 16:23:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641216/SRX10641216.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:23:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641216/SRX10641216.05_summits.bed INFO @ Wed, 08 Dec 2021 16:23:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (431 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 16:23:19: 11000000 INFO @ Wed, 08 Dec 2021 16:23:21: 14000000 INFO @ Wed, 08 Dec 2021 16:23:30: 12000000 INFO @ Wed, 08 Dec 2021 16:23:32: 15000000 INFO @ Wed, 08 Dec 2021 16:23:33: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 16:23:33: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 16:23:33: #1 total tags in treatment: 4541633 INFO @ Wed, 08 Dec 2021 16:23:33: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:23:33: #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 16:23:33: #1 tags after filtering in treatment: 4245177 INFO @ Wed, 08 Dec 2021 16:23:33: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 16:23:33: #1 finished! INFO @ Wed, 08 Dec 2021 16:23:33: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:23:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:23:33: #2 number of paired peaks: 427 WARNING @ Wed, 08 Dec 2021 16:23:33: Fewer paired peaks (427) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 427 pairs to build model! INFO @ Wed, 08 Dec 2021 16:23:33: start model_add_line... INFO @ Wed, 08 Dec 2021 16:23:33: start X-correlation... INFO @ Wed, 08 Dec 2021 16:23:33: end of X-cor INFO @ Wed, 08 Dec 2021 16:23:33: #2 finished! INFO @ Wed, 08 Dec 2021 16:23:33: #2 predicted fragment length is 223 bps INFO @ Wed, 08 Dec 2021 16:23:33: #2 alternative fragment length(s) may be 223 bps INFO @ Wed, 08 Dec 2021 16:23:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641216/SRX10641216.10_model.r WARNING @ Wed, 08 Dec 2021 16:23:33: #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 16:23:33: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Wed, 08 Dec 2021 16:23:33: #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 16:23:33: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:23:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:23:41: 13000000 INFO @ Wed, 08 Dec 2021 16:23:43: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:23:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641216/SRX10641216.10_peaks.xls INFO @ Wed, 08 Dec 2021 16:23:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641216/SRX10641216.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:23:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641216/SRX10641216.10_summits.bed INFO @ Wed, 08 Dec 2021 16:23:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (236 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 16:23:51: 14000000 INFO @ Wed, 08 Dec 2021 16:24:01: 15000000 INFO @ Wed, 08 Dec 2021 16:24:01: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 16:24:01: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 16:24:01: #1 total tags in treatment: 4541633 INFO @ Wed, 08 Dec 2021 16:24:01: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:24:01: #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 16:24:02: #1 tags after filtering in treatment: 4245177 INFO @ Wed, 08 Dec 2021 16:24:02: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 16:24:02: #1 finished! INFO @ Wed, 08 Dec 2021 16:24:02: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:24:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:24:02: #2 number of paired peaks: 427 WARNING @ Wed, 08 Dec 2021 16:24:02: Fewer paired peaks (427) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 427 pairs to build model! INFO @ Wed, 08 Dec 2021 16:24:02: start model_add_line... INFO @ Wed, 08 Dec 2021 16:24:02: start X-correlation... INFO @ Wed, 08 Dec 2021 16:24:02: end of X-cor INFO @ Wed, 08 Dec 2021 16:24:02: #2 finished! INFO @ Wed, 08 Dec 2021 16:24:02: #2 predicted fragment length is 223 bps INFO @ Wed, 08 Dec 2021 16:24:02: #2 alternative fragment length(s) may be 223 bps INFO @ Wed, 08 Dec 2021 16:24:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641216/SRX10641216.20_model.r WARNING @ Wed, 08 Dec 2021 16:24:02: #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 16:24:02: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Wed, 08 Dec 2021 16:24:02: #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 16:24:02: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:24:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:24:12: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:24:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641216/SRX10641216.20_peaks.xls INFO @ Wed, 08 Dec 2021 16:24:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641216/SRX10641216.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:24:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641216/SRX10641216.20_summits.bed INFO @ Wed, 08 Dec 2021 16:24:16: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (163 records, 4 fields): 3 millis CompletedMACS2peakCalling