Job ID = 8070268 SRX = SRX8392432 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: 00:10:47 7913909 reads; of these: 7913909 (100.00%) were paired; of these: 3508372 (44.33%) aligned concordantly 0 times 3862363 (48.80%) aligned concordantly exactly 1 time 543174 (6.86%) aligned concordantly >1 times ---- 3508372 pairs aligned concordantly 0 times; of these: 1005420 (28.66%) aligned discordantly 1 time ---- 2502952 pairs aligned 0 times concordantly or discordantly; of these: 5005904 mates make up the pairs; of these: 4703378 (93.96%) aligned 0 times 127123 (2.54%) aligned exactly 1 time 175403 (3.50%) aligned >1 times 70.28% overall alignment rate Time searching: 00:10:47 Overall time: 00:10:47 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] 1131376 / 5366223 = 0.2108 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 13:17:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392432/SRX8392432.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392432/SRX8392432.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392432/SRX8392432.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392432/SRX8392432.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 13:17:33: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:17:33: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:17:41: 1000000 INFO @ Sat, 08 Aug 2020 13:17:48: 2000000 INFO @ Sat, 08 Aug 2020 13:17:56: 3000000 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 13:18:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392432/SRX8392432.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392432/SRX8392432.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392432/SRX8392432.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392432/SRX8392432.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 13:18:03: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:18:03: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:18:04: 4000000 INFO @ Sat, 08 Aug 2020 13:18:10: 1000000 INFO @ Sat, 08 Aug 2020 13:18:12: 5000000 INFO @ Sat, 08 Aug 2020 13:18:18: 2000000 INFO @ Sat, 08 Aug 2020 13:18:20: 6000000 INFO @ Sat, 08 Aug 2020 13:18:25: 3000000 INFO @ Sat, 08 Aug 2020 13:18:28: 7000000 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 13:18:32: 4000000 INFO @ Sat, 08 Aug 2020 13:18:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392432/SRX8392432.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392432/SRX8392432.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392432/SRX8392432.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392432/SRX8392432.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 13:18:33: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:18:33: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:18:36: 8000000 INFO @ Sat, 08 Aug 2020 13:18:39: 5000000 INFO @ Sat, 08 Aug 2020 13:18:40: 1000000 INFO @ Sat, 08 Aug 2020 13:18:43: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:18:43: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:18:43: #1 total tags in treatment: 3437186 INFO @ Sat, 08 Aug 2020 13:18:43: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:18:43: #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 13:18:43: #1 tags after filtering in treatment: 3046581 INFO @ Sat, 08 Aug 2020 13:18:43: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 08 Aug 2020 13:18:43: #1 finished! INFO @ Sat, 08 Aug 2020 13:18:43: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:18:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:18:44: #2 number of paired peaks: 2819 INFO @ Sat, 08 Aug 2020 13:18:44: start model_add_line... INFO @ Sat, 08 Aug 2020 13:18:44: start X-correlation... INFO @ Sat, 08 Aug 2020 13:18:44: end of X-cor INFO @ Sat, 08 Aug 2020 13:18:44: #2 finished! INFO @ Sat, 08 Aug 2020 13:18:44: #2 predicted fragment length is 201 bps INFO @ Sat, 08 Aug 2020 13:18:44: #2 alternative fragment length(s) may be 201 bps INFO @ Sat, 08 Aug 2020 13:18:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392432/SRX8392432.05_model.r WARNING @ Sat, 08 Aug 2020 13:18:44: #2 Since the d (201) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:18:44: #2 You may need to consider one of the other alternative d(s): 201 WARNING @ Sat, 08 Aug 2020 13:18:44: #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 13:18:44: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:18:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:18:46: 6000000 INFO @ Sat, 08 Aug 2020 13:18:47: 2000000 INFO @ Sat, 08 Aug 2020 13:18:51: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:18:53: 7000000 INFO @ Sat, 08 Aug 2020 13:18:54: 3000000 INFO @ Sat, 08 Aug 2020 13:18:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392432/SRX8392432.05_peaks.xls INFO @ Sat, 08 Aug 2020 13:18:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392432/SRX8392432.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:18:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392432/SRX8392432.05_summits.bed INFO @ Sat, 08 Aug 2020 13:18:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5916 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:18:59: 8000000 INFO @ Sat, 08 Aug 2020 13:19:01: 4000000 INFO @ Sat, 08 Aug 2020 13:19:05: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:19:05: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:19:05: #1 total tags in treatment: 3437186 INFO @ Sat, 08 Aug 2020 13:19:05: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:19:05: #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 13:19:05: #1 tags after filtering in treatment: 3046581 INFO @ Sat, 08 Aug 2020 13:19:05: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 08 Aug 2020 13:19:05: #1 finished! INFO @ Sat, 08 Aug 2020 13:19:05: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:19:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:19:06: #2 number of paired peaks: 2819 INFO @ Sat, 08 Aug 2020 13:19:06: start model_add_line... INFO @ Sat, 08 Aug 2020 13:19:06: start X-correlation... INFO @ Sat, 08 Aug 2020 13:19:06: end of X-cor INFO @ Sat, 08 Aug 2020 13:19:06: #2 finished! INFO @ Sat, 08 Aug 2020 13:19:06: #2 predicted fragment length is 201 bps INFO @ Sat, 08 Aug 2020 13:19:06: #2 alternative fragment length(s) may be 201 bps INFO @ Sat, 08 Aug 2020 13:19:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392432/SRX8392432.10_model.r WARNING @ Sat, 08 Aug 2020 13:19:06: #2 Since the d (201) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:19:06: #2 You may need to consider one of the other alternative d(s): 201 WARNING @ Sat, 08 Aug 2020 13:19:06: #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 13:19:06: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:19:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:19:08: 5000000 INFO @ Sat, 08 Aug 2020 13:19:14: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:19:15: 6000000 INFO @ Sat, 08 Aug 2020 13:19:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392432/SRX8392432.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:19:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392432/SRX8392432.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:19:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392432/SRX8392432.10_summits.bed INFO @ Sat, 08 Aug 2020 13:19:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3462 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:19:22: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 13:19:28: 8000000 INFO @ Sat, 08 Aug 2020 13:19:34: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:19:34: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:19:34: #1 total tags in treatment: 3437186 INFO @ Sat, 08 Aug 2020 13:19:34: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:19:34: #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 13:19:34: #1 tags after filtering in treatment: 3046581 INFO @ Sat, 08 Aug 2020 13:19:34: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 08 Aug 2020 13:19:34: #1 finished! INFO @ Sat, 08 Aug 2020 13:19:34: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:19:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:19:34: #2 number of paired peaks: 2819 INFO @ Sat, 08 Aug 2020 13:19:34: start model_add_line... INFO @ Sat, 08 Aug 2020 13:19:34: start X-correlation... INFO @ Sat, 08 Aug 2020 13:19:34: end of X-cor INFO @ Sat, 08 Aug 2020 13:19:34: #2 finished! INFO @ Sat, 08 Aug 2020 13:19:34: #2 predicted fragment length is 201 bps INFO @ Sat, 08 Aug 2020 13:19:34: #2 alternative fragment length(s) may be 201 bps INFO @ Sat, 08 Aug 2020 13:19:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392432/SRX8392432.20_model.r WARNING @ Sat, 08 Aug 2020 13:19:34: #2 Since the d (201) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:19:34: #2 You may need to consider one of the other alternative d(s): 201 WARNING @ Sat, 08 Aug 2020 13:19:34: #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 13:19:34: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:19:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:19:42: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:19:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392432/SRX8392432.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:19:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392432/SRX8392432.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:19:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392432/SRX8392432.20_summits.bed INFO @ Sat, 08 Aug 2020 13:19:45: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1894 records, 4 fields): 4 millis CompletedMACS2peakCalling