Job ID = 14159686 SRX = SRX8845628 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: 00:05:35 6488747 reads; of these: 6488747 (100.00%) were paired; of these: 2151824 (33.16%) aligned concordantly 0 times 3810437 (58.72%) aligned concordantly exactly 1 time 526486 (8.11%) aligned concordantly >1 times ---- 2151824 pairs aligned concordantly 0 times; of these: 658146 (30.59%) aligned discordantly 1 time ---- 1493678 pairs aligned 0 times concordantly or discordantly; of these: 2987356 mates make up the pairs; of these: 2633489 (88.15%) aligned 0 times 197889 (6.62%) aligned exactly 1 time 155978 (5.22%) aligned >1 times 79.71% overall alignment rate Time searching: 00:05:35 Overall time: 00:05:35 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 8 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] 452688 / 4957541 = 0.0913 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 00:29:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845628/SRX8845628.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845628/SRX8845628.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845628/SRX8845628.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845628/SRX8845628.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 00:29:51: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:29:51: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:29:57: 1000000 INFO @ Thu, 09 Dec 2021 00:30:04: 2000000 INFO @ Thu, 09 Dec 2021 00:30:10: 3000000 INFO @ Thu, 09 Dec 2021 00:30:16: 4000000 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 00:30:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845628/SRX8845628.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845628/SRX8845628.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845628/SRX8845628.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845628/SRX8845628.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 00:30:21: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:30:21: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:30:22: 5000000 INFO @ Thu, 09 Dec 2021 00:30:28: 1000000 INFO @ Thu, 09 Dec 2021 00:30:28: 6000000 INFO @ Thu, 09 Dec 2021 00:30:34: 7000000 INFO @ Thu, 09 Dec 2021 00:30:35: 2000000 INFO @ Thu, 09 Dec 2021 00:30:40: 8000000 INFO @ Thu, 09 Dec 2021 00:30:41: 3000000 INFO @ Thu, 09 Dec 2021 00:30:47: 9000000 INFO @ Thu, 09 Dec 2021 00:30:48: 4000000 BedGraph に変換中... INFO @ Thu, 09 Dec 2021 00:30:49: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 00:30:49: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 00:30:49: #1 total tags in treatment: 3945291 INFO @ Thu, 09 Dec 2021 00:30:49: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:30:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) 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 00:30:49: #1 tags after filtering in treatment: 3211053 INFO @ Thu, 09 Dec 2021 00:30:49: #1 Redundant rate of treatment: 0.19 INFO @ Thu, 09 Dec 2021 00:30:49: #1 finished! INFO @ Thu, 09 Dec 2021 00:30:49: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:30:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:30:50: #2 number of paired peaks: 1907 INFO @ Thu, 09 Dec 2021 00:30:50: start model_add_line... INFO @ Thu, 09 Dec 2021 00:30:50: start X-correlation... INFO @ Thu, 09 Dec 2021 00:30:50: end of X-cor INFO @ Thu, 09 Dec 2021 00:30:50: #2 finished! INFO @ Thu, 09 Dec 2021 00:30:50: #2 predicted fragment length is 112 bps INFO @ Thu, 09 Dec 2021 00:30:50: #2 alternative fragment length(s) may be 112 bps INFO @ Thu, 09 Dec 2021 00:30:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845628/SRX8845628.05_model.r WARNING @ Thu, 09 Dec 2021 00:30:50: #2 Since the d (112) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:30:50: #2 You may need to consider one of the other alternative d(s): 112 WARNING @ Thu, 09 Dec 2021 00:30:50: #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 00:30:50: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:30:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:30:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845628/SRX8845628.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845628/SRX8845628.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845628/SRX8845628.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845628/SRX8845628.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 00:30:51: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:30:51: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:30:54: 5000000 INFO @ Thu, 09 Dec 2021 00:30:57: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:30:57: 1000000 INFO @ Thu, 09 Dec 2021 00:31:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845628/SRX8845628.05_peaks.xls INFO @ Thu, 09 Dec 2021 00:31:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845628/SRX8845628.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:31:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845628/SRX8845628.05_summits.bed INFO @ Thu, 09 Dec 2021 00:31:01: Done! INFO @ Thu, 09 Dec 2021 00:31:01: 6000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5628 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:31:04: 2000000 INFO @ Thu, 09 Dec 2021 00:31:07: 7000000 INFO @ Thu, 09 Dec 2021 00:31:10: 3000000 INFO @ Thu, 09 Dec 2021 00:31:14: 8000000 INFO @ Thu, 09 Dec 2021 00:31:16: 4000000 INFO @ Thu, 09 Dec 2021 00:31:20: 9000000 INFO @ Thu, 09 Dec 2021 00:31:22: 5000000 INFO @ Thu, 09 Dec 2021 00:31:23: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 00:31:23: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 00:31:23: #1 total tags in treatment: 3945291 INFO @ Thu, 09 Dec 2021 00:31:23: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:31:23: #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 00:31:23: #1 tags after filtering in treatment: 3211053 INFO @ Thu, 09 Dec 2021 00:31:23: #1 Redundant rate of treatment: 0.19 INFO @ Thu, 09 Dec 2021 00:31:23: #1 finished! INFO @ Thu, 09 Dec 2021 00:31:23: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:31:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:31:24: #2 number of paired peaks: 1907 INFO @ Thu, 09 Dec 2021 00:31:24: start model_add_line... INFO @ Thu, 09 Dec 2021 00:31:24: start X-correlation... INFO @ Thu, 09 Dec 2021 00:31:24: end of X-cor INFO @ Thu, 09 Dec 2021 00:31:24: #2 finished! INFO @ Thu, 09 Dec 2021 00:31:24: #2 predicted fragment length is 112 bps INFO @ Thu, 09 Dec 2021 00:31:24: #2 alternative fragment length(s) may be 112 bps INFO @ Thu, 09 Dec 2021 00:31:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845628/SRX8845628.10_model.r WARNING @ Thu, 09 Dec 2021 00:31:24: #2 Since the d (112) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:31:24: #2 You may need to consider one of the other alternative d(s): 112 WARNING @ Thu, 09 Dec 2021 00:31:24: #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 00:31:24: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:31:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:31:29: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 00:31:31: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:31:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845628/SRX8845628.10_peaks.xls INFO @ Thu, 09 Dec 2021 00:31:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845628/SRX8845628.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:31:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845628/SRX8845628.10_summits.bed INFO @ Thu, 09 Dec 2021 00:31:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3424 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:31:35: 7000000 INFO @ Thu, 09 Dec 2021 00:31:41: 8000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 00:31:47: 9000000 INFO @ Thu, 09 Dec 2021 00:31:49: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 00:31:49: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 00:31:49: #1 total tags in treatment: 3945291 INFO @ Thu, 09 Dec 2021 00:31:49: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:31:49: #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 00:31:49: #1 tags after filtering in treatment: 3211053 INFO @ Thu, 09 Dec 2021 00:31:49: #1 Redundant rate of treatment: 0.19 INFO @ Thu, 09 Dec 2021 00:31:49: #1 finished! INFO @ Thu, 09 Dec 2021 00:31:49: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:31:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:31:50: #2 number of paired peaks: 1907 INFO @ Thu, 09 Dec 2021 00:31:50: start model_add_line... INFO @ Thu, 09 Dec 2021 00:31:50: start X-correlation... INFO @ Thu, 09 Dec 2021 00:31:50: end of X-cor INFO @ Thu, 09 Dec 2021 00:31:50: #2 finished! INFO @ Thu, 09 Dec 2021 00:31:50: #2 predicted fragment length is 112 bps INFO @ Thu, 09 Dec 2021 00:31:50: #2 alternative fragment length(s) may be 112 bps INFO @ Thu, 09 Dec 2021 00:31:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845628/SRX8845628.20_model.r WARNING @ Thu, 09 Dec 2021 00:31:50: #2 Since the d (112) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:31:50: #2 You may need to consider one of the other alternative d(s): 112 WARNING @ Thu, 09 Dec 2021 00:31:50: #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 00:31:50: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:31:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:31:57: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:32:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845628/SRX8845628.20_peaks.xls INFO @ Thu, 09 Dec 2021 00:32:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845628/SRX8845628.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:32:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845628/SRX8845628.20_summits.bed INFO @ Thu, 09 Dec 2021 00:32:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1636 records, 4 fields): 3 millis CompletedMACS2peakCalling