Job ID = 14158209 SRX = SRX10641203 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: 00:20:32 18949906 reads; of these: 18949906 (100.00%) were paired; of these: 14637389 (77.24%) aligned concordantly 0 times 2610739 (13.78%) aligned concordantly exactly 1 time 1701778 (8.98%) aligned concordantly >1 times ---- 14637389 pairs aligned concordantly 0 times; of these: 1109677 (7.58%) aligned discordantly 1 time ---- 13527712 pairs aligned 0 times concordantly or discordantly; of these: 27055424 mates make up the pairs; of these: 26405413 (97.60%) aligned 0 times 330495 (1.22%) aligned exactly 1 time 319516 (1.18%) aligned >1 times 30.33% overall alignment rate Time searching: 00:20:32 Overall time: 00:20:32 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 12 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] 1104354 / 5400253 = 0.2045 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 15:15:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641203/SRX10641203.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641203/SRX10641203.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641203/SRX10641203.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641203/SRX10641203.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 15:15:34: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:15:34: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:15:44: 1000000 INFO @ Wed, 08 Dec 2021 15:15:53: 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 15:16:03: 3000000 INFO @ Wed, 08 Dec 2021 15:16:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641203/SRX10641203.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641203/SRX10641203.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641203/SRX10641203.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641203/SRX10641203.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 15:16:04: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:16:04: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:16:13: 1000000 INFO @ Wed, 08 Dec 2021 15:16:13: 4000000 INFO @ Wed, 08 Dec 2021 15:16:21: 2000000 INFO @ Wed, 08 Dec 2021 15:16:23: 5000000 INFO @ Wed, 08 Dec 2021 15:16:29: 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 15:16:33: 6000000 INFO @ Wed, 08 Dec 2021 15:16:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641203/SRX10641203.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641203/SRX10641203.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641203/SRX10641203.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641203/SRX10641203.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 15:16:34: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:16:34: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:16:38: 4000000 INFO @ Wed, 08 Dec 2021 15:16:43: 1000000 INFO @ Wed, 08 Dec 2021 15:16:44: 7000000 INFO @ Wed, 08 Dec 2021 15:16:46: 5000000 INFO @ Wed, 08 Dec 2021 15:16:51: 2000000 INFO @ Wed, 08 Dec 2021 15:16:54: 8000000 INFO @ Wed, 08 Dec 2021 15:16:55: 6000000 INFO @ Wed, 08 Dec 2021 15:17:00: 3000000 INFO @ Wed, 08 Dec 2021 15:17:03: 7000000 INFO @ Wed, 08 Dec 2021 15:17:04: 9000000 INFO @ Wed, 08 Dec 2021 15:17:07: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 15:17:07: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 15:17:07: #1 total tags in treatment: 3337087 INFO @ Wed, 08 Dec 2021 15:17:07: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:17:07: #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 15:17:07: #1 tags after filtering in treatment: 2547615 INFO @ Wed, 08 Dec 2021 15:17:07: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 08 Dec 2021 15:17:07: #1 finished! INFO @ Wed, 08 Dec 2021 15:17:07: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:17:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:17:07: #2 number of paired peaks: 990 WARNING @ Wed, 08 Dec 2021 15:17:07: Fewer paired peaks (990) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 990 pairs to build model! INFO @ Wed, 08 Dec 2021 15:17:07: start model_add_line... INFO @ Wed, 08 Dec 2021 15:17:07: start X-correlation... INFO @ Wed, 08 Dec 2021 15:17:08: end of X-cor INFO @ Wed, 08 Dec 2021 15:17:08: #2 finished! INFO @ Wed, 08 Dec 2021 15:17:08: #2 predicted fragment length is 257 bps INFO @ Wed, 08 Dec 2021 15:17:08: #2 alternative fragment length(s) may be 257 bps INFO @ Wed, 08 Dec 2021 15:17:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641203/SRX10641203.05_model.r WARNING @ Wed, 08 Dec 2021 15:17:08: #2 Since the d (257) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 15:17:08: #2 You may need to consider one of the other alternative d(s): 257 WARNING @ Wed, 08 Dec 2021 15:17:08: #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 15:17:08: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:17:08: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:17:09: 4000000 INFO @ Wed, 08 Dec 2021 15:17:12: 8000000 INFO @ Wed, 08 Dec 2021 15:17:15: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:17:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641203/SRX10641203.05_peaks.xls INFO @ Wed, 08 Dec 2021 15:17:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641203/SRX10641203.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:17:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641203/SRX10641203.05_summits.bed INFO @ Wed, 08 Dec 2021 15:17:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (826 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 15:17:18: 5000000 INFO @ Wed, 08 Dec 2021 15:17:20: 9000000 INFO @ Wed, 08 Dec 2021 15:17:22: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 15:17:22: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 15:17:22: #1 total tags in treatment: 3337087 INFO @ Wed, 08 Dec 2021 15:17:22: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:17:22: #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 15:17:22: #1 tags after filtering in treatment: 2547615 INFO @ Wed, 08 Dec 2021 15:17:22: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 08 Dec 2021 15:17:22: #1 finished! INFO @ Wed, 08 Dec 2021 15:17:22: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:17:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:17:23: #2 number of paired peaks: 990 WARNING @ Wed, 08 Dec 2021 15:17:23: Fewer paired peaks (990) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 990 pairs to build model! INFO @ Wed, 08 Dec 2021 15:17:23: start model_add_line... INFO @ Wed, 08 Dec 2021 15:17:23: start X-correlation... INFO @ Wed, 08 Dec 2021 15:17:23: end of X-cor INFO @ Wed, 08 Dec 2021 15:17:23: #2 finished! INFO @ Wed, 08 Dec 2021 15:17:23: #2 predicted fragment length is 257 bps INFO @ Wed, 08 Dec 2021 15:17:23: #2 alternative fragment length(s) may be 257 bps INFO @ Wed, 08 Dec 2021 15:17:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641203/SRX10641203.10_model.r WARNING @ Wed, 08 Dec 2021 15:17:23: #2 Since the d (257) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 15:17:23: #2 You may need to consider one of the other alternative d(s): 257 WARNING @ Wed, 08 Dec 2021 15:17:23: #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 15:17:23: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:17:23: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 15:17:26: 6000000 INFO @ Wed, 08 Dec 2021 15:17:30: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:17:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641203/SRX10641203.10_peaks.xls INFO @ Wed, 08 Dec 2021 15:17:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641203/SRX10641203.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:17:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641203/SRX10641203.10_summits.bed INFO @ Wed, 08 Dec 2021 15:17:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (585 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 15:17:34: 7000000 INFO @ Wed, 08 Dec 2021 15:17:41: 8000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 15:17:49: 9000000 INFO @ Wed, 08 Dec 2021 15:17:51: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 15:17:51: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 15:17:51: #1 total tags in treatment: 3337087 INFO @ Wed, 08 Dec 2021 15:17:51: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:17:51: #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 15:17:51: #1 tags after filtering in treatment: 2547615 INFO @ Wed, 08 Dec 2021 15:17:51: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 08 Dec 2021 15:17:51: #1 finished! INFO @ Wed, 08 Dec 2021 15:17:51: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:17:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:17:51: #2 number of paired peaks: 990 WARNING @ Wed, 08 Dec 2021 15:17:51: Fewer paired peaks (990) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 990 pairs to build model! INFO @ Wed, 08 Dec 2021 15:17:51: start model_add_line... INFO @ Wed, 08 Dec 2021 15:17:51: start X-correlation... INFO @ Wed, 08 Dec 2021 15:17:51: end of X-cor INFO @ Wed, 08 Dec 2021 15:17:51: #2 finished! INFO @ Wed, 08 Dec 2021 15:17:51: #2 predicted fragment length is 257 bps INFO @ Wed, 08 Dec 2021 15:17:51: #2 alternative fragment length(s) may be 257 bps INFO @ Wed, 08 Dec 2021 15:17:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641203/SRX10641203.20_model.r WARNING @ Wed, 08 Dec 2021 15:17:51: #2 Since the d (257) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 15:17:51: #2 You may need to consider one of the other alternative d(s): 257 WARNING @ Wed, 08 Dec 2021 15:17:51: #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 15:17:51: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:17:51: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:17:58: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:18:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641203/SRX10641203.20_peaks.xls INFO @ Wed, 08 Dec 2021 15:18:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641203/SRX10641203.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:18:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641203/SRX10641203.20_summits.bed INFO @ Wed, 08 Dec 2021 15:18:01: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (407 records, 4 fields): 4 millis CompletedMACS2peakCalling