Job ID = 8070425 SRX = SRX8392431 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: 00:14:21 10228115 reads; of these: 10228115 (100.00%) were paired; of these: 4696691 (45.92%) aligned concordantly 0 times 4962171 (48.52%) aligned concordantly exactly 1 time 569253 (5.57%) aligned concordantly >1 times ---- 4696691 pairs aligned concordantly 0 times; of these: 1571018 (33.45%) aligned discordantly 1 time ---- 3125673 pairs aligned 0 times concordantly or discordantly; of these: 6251346 mates make up the pairs; of these: 5849167 (93.57%) aligned 0 times 163147 (2.61%) aligned exactly 1 time 239032 (3.82%) aligned >1 times 71.41% overall alignment rate Time searching: 00:14:21 Overall time: 00:14:21 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 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] 1625452 / 7034304 = 0.2311 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 08 Aug 2020 13:26:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392431/SRX8392431.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392431/SRX8392431.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392431/SRX8392431.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392431/SRX8392431.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 @ Sat, 08 Aug 2020 13:26:13: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:26:13: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:26:23: 1000000 INFO @ Sat, 08 Aug 2020 13:26:34: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 08 Aug 2020 13:26:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392431/SRX8392431.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392431/SRX8392431.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392431/SRX8392431.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392431/SRX8392431.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 @ Sat, 08 Aug 2020 13:26:43: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:26:43: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:26:44: 3000000 INFO @ Sat, 08 Aug 2020 13:26:54: 1000000 INFO @ Sat, 08 Aug 2020 13:26:56: 4000000 INFO @ Sat, 08 Aug 2020 13:27:05: 2000000 INFO @ Sat, 08 Aug 2020 13:27:09: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 08 Aug 2020 13:27:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392431/SRX8392431.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392431/SRX8392431.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392431/SRX8392431.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392431/SRX8392431.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 @ Sat, 08 Aug 2020 13:27:13: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:27:13: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:27:17: 3000000 INFO @ Sat, 08 Aug 2020 13:27:22: 6000000 INFO @ Sat, 08 Aug 2020 13:27:25: 1000000 INFO @ Sat, 08 Aug 2020 13:27:29: 4000000 INFO @ Sat, 08 Aug 2020 13:27:34: 7000000 INFO @ Sat, 08 Aug 2020 13:27:38: 2000000 INFO @ Sat, 08 Aug 2020 13:27:41: 5000000 INFO @ Sat, 08 Aug 2020 13:27:47: 8000000 INFO @ Sat, 08 Aug 2020 13:27:49: 3000000 INFO @ Sat, 08 Aug 2020 13:27:52: 6000000 INFO @ Sat, 08 Aug 2020 13:28:00: 9000000 INFO @ Sat, 08 Aug 2020 13:28:00: 4000000 INFO @ Sat, 08 Aug 2020 13:28:03: 7000000 INFO @ Sat, 08 Aug 2020 13:28:12: 10000000 INFO @ Sat, 08 Aug 2020 13:28:13: 5000000 INFO @ Sat, 08 Aug 2020 13:28:14: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 13:28:25: 9000000 INFO @ Sat, 08 Aug 2020 13:28:25: 11000000 INFO @ Sat, 08 Aug 2020 13:28:25: 6000000 INFO @ Sat, 08 Aug 2020 13:28:30: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:28:30: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:28:30: #1 total tags in treatment: 4193540 INFO @ Sat, 08 Aug 2020 13:28:30: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:28:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:28:30: #1 tags after filtering in treatment: 3612896 INFO @ Sat, 08 Aug 2020 13:28:30: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 08 Aug 2020 13:28:30: #1 finished! INFO @ Sat, 08 Aug 2020 13:28:30: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:28:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:28:30: #2 number of paired peaks: 3735 INFO @ Sat, 08 Aug 2020 13:28:30: start model_add_line... INFO @ Sat, 08 Aug 2020 13:28:30: start X-correlation... INFO @ Sat, 08 Aug 2020 13:28:30: end of X-cor INFO @ Sat, 08 Aug 2020 13:28:30: #2 finished! INFO @ Sat, 08 Aug 2020 13:28:30: #2 predicted fragment length is 195 bps INFO @ Sat, 08 Aug 2020 13:28:30: #2 alternative fragment length(s) may be 195 bps INFO @ Sat, 08 Aug 2020 13:28:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392431/SRX8392431.05_model.r WARNING @ Sat, 08 Aug 2020 13:28:30: #2 Since the d (195) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:28:30: #2 You may need to consider one of the other alternative d(s): 195 WARNING @ Sat, 08 Aug 2020 13:28:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 13:28:30: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:28:30: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:28:36: 10000000 INFO @ Sat, 08 Aug 2020 13:28:38: 7000000 INFO @ Sat, 08 Aug 2020 13:28:40: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:28:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392431/SRX8392431.05_peaks.xls INFO @ Sat, 08 Aug 2020 13:28:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392431/SRX8392431.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:28:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392431/SRX8392431.05_summits.bed INFO @ Sat, 08 Aug 2020 13:28:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (7892 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:28:47: 11000000 INFO @ Sat, 08 Aug 2020 13:28:50: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:28:50: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:28:50: #1 total tags in treatment: 4193540 INFO @ Sat, 08 Aug 2020 13:28:50: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:28:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:28:50: #1 tags after filtering in treatment: 3612896 INFO @ Sat, 08 Aug 2020 13:28:50: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 08 Aug 2020 13:28:50: #1 finished! INFO @ Sat, 08 Aug 2020 13:28:50: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:28:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:28:50: 8000000 INFO @ Sat, 08 Aug 2020 13:28:51: #2 number of paired peaks: 3735 INFO @ Sat, 08 Aug 2020 13:28:51: start model_add_line... INFO @ Sat, 08 Aug 2020 13:28:51: start X-correlation... INFO @ Sat, 08 Aug 2020 13:28:51: end of X-cor INFO @ Sat, 08 Aug 2020 13:28:51: #2 finished! INFO @ Sat, 08 Aug 2020 13:28:51: #2 predicted fragment length is 195 bps INFO @ Sat, 08 Aug 2020 13:28:51: #2 alternative fragment length(s) may be 195 bps INFO @ Sat, 08 Aug 2020 13:28:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392431/SRX8392431.10_model.r WARNING @ Sat, 08 Aug 2020 13:28:51: #2 Since the d (195) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:28:51: #2 You may need to consider one of the other alternative d(s): 195 WARNING @ Sat, 08 Aug 2020 13:28:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 13:28:51: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:28:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:29:00: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:29:02: 9000000 INFO @ Sat, 08 Aug 2020 13:29:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392431/SRX8392431.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:29:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392431/SRX8392431.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:29:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392431/SRX8392431.10_summits.bed INFO @ Sat, 08 Aug 2020 13:29:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5120 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:29:13: 10000000 INFO @ Sat, 08 Aug 2020 13:29:24: 11000000 INFO @ Sat, 08 Aug 2020 13:29:28: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:29:28: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:29:28: #1 total tags in treatment: 4193540 INFO @ Sat, 08 Aug 2020 13:29:28: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:29:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:29:28: #1 tags after filtering in treatment: 3612896 INFO @ Sat, 08 Aug 2020 13:29:28: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 08 Aug 2020 13:29:28: #1 finished! INFO @ Sat, 08 Aug 2020 13:29:28: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:29:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:29:29: #2 number of paired peaks: 3735 INFO @ Sat, 08 Aug 2020 13:29:29: start model_add_line... INFO @ Sat, 08 Aug 2020 13:29:29: start X-correlation... INFO @ Sat, 08 Aug 2020 13:29:29: end of X-cor INFO @ Sat, 08 Aug 2020 13:29:29: #2 finished! INFO @ Sat, 08 Aug 2020 13:29:29: #2 predicted fragment length is 195 bps INFO @ Sat, 08 Aug 2020 13:29:29: #2 alternative fragment length(s) may be 195 bps INFO @ Sat, 08 Aug 2020 13:29:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392431/SRX8392431.20_model.r WARNING @ Sat, 08 Aug 2020 13:29:29: #2 Since the d (195) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:29:29: #2 You may need to consider one of the other alternative d(s): 195 WARNING @ Sat, 08 Aug 2020 13:29:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 13:29:29: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:29:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:29:39: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:29:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392431/SRX8392431.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:29:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392431/SRX8392431.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:29:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392431/SRX8392431.20_summits.bed INFO @ Sat, 08 Aug 2020 13:29:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2910 records, 4 fields): 16 millis CompletedMACS2peakCalling