Job ID = 8069683 SRX = SRX8392428 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: 00:00:01 Multiseed full-index search: 00:02:24 1769208 reads; of these: 1769208 (100.00%) were paired; of these: 828612 (46.84%) aligned concordantly 0 times 838649 (47.40%) aligned concordantly exactly 1 time 101947 (5.76%) aligned concordantly >1 times ---- 828612 pairs aligned concordantly 0 times; of these: 233454 (28.17%) aligned discordantly 1 time ---- 595158 pairs aligned 0 times concordantly or discordantly; of these: 1190316 mates make up the pairs; of these: 1127210 (94.70%) aligned 0 times 25855 (2.17%) aligned exactly 1 time 37251 (3.13%) aligned >1 times 68.14% overall alignment rate Time searching: 00:02:25 Overall time: 00:02:25 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_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] 213029 / 1163251 = 0.1831 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 12:48:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392428/SRX8392428.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392428/SRX8392428.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392428/SRX8392428.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392428/SRX8392428.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 12:48:46: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:48:46: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:48:56: 1000000 INFO @ Sat, 08 Aug 2020 12:49:06: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:49:06: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:49:06: #1 total tags in treatment: 760761 INFO @ Sat, 08 Aug 2020 12:49:06: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:49:06: #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 12:49:06: #1 tags after filtering in treatment: 729607 INFO @ Sat, 08 Aug 2020 12:49:06: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 08 Aug 2020 12:49:06: #1 finished! INFO @ Sat, 08 Aug 2020 12:49:06: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:49:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:49:06: #2 number of paired peaks: 2858 INFO @ Sat, 08 Aug 2020 12:49:06: start model_add_line... INFO @ Sat, 08 Aug 2020 12:49:06: start X-correlation... INFO @ Sat, 08 Aug 2020 12:49:06: end of X-cor INFO @ Sat, 08 Aug 2020 12:49:06: #2 finished! INFO @ Sat, 08 Aug 2020 12:49:06: #2 predicted fragment length is 193 bps INFO @ Sat, 08 Aug 2020 12:49:06: #2 alternative fragment length(s) may be 193 bps INFO @ Sat, 08 Aug 2020 12:49:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392428/SRX8392428.05_model.r WARNING @ Sat, 08 Aug 2020 12:49:06: #2 Since the d (193) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:49:06: #2 You may need to consider one of the other alternative d(s): 193 WARNING @ Sat, 08 Aug 2020 12:49:06: #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 12:49:06: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:49:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:49:08: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:49:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392428/SRX8392428.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:49:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392428/SRX8392428.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:49:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392428/SRX8392428.05_summits.bed INFO @ Sat, 08 Aug 2020 12:49:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1918 records, 4 fields): 12 millis CompletedMACS2peakCalling 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 12:49:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392428/SRX8392428.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392428/SRX8392428.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392428/SRX8392428.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392428/SRX8392428.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 12:49:16: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:49:16: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:49:26: 1000000 INFO @ Sat, 08 Aug 2020 12:49:36: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:49:36: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:49:36: #1 total tags in treatment: 760761 INFO @ Sat, 08 Aug 2020 12:49:36: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:49:36: #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 12:49:36: #1 tags after filtering in treatment: 729607 INFO @ Sat, 08 Aug 2020 12:49:36: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 08 Aug 2020 12:49:36: #1 finished! INFO @ Sat, 08 Aug 2020 12:49:36: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:49:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:49:36: #2 number of paired peaks: 2858 INFO @ Sat, 08 Aug 2020 12:49:36: start model_add_line... INFO @ Sat, 08 Aug 2020 12:49:36: start X-correlation... INFO @ Sat, 08 Aug 2020 12:49:36: end of X-cor INFO @ Sat, 08 Aug 2020 12:49:36: #2 finished! INFO @ Sat, 08 Aug 2020 12:49:36: #2 predicted fragment length is 193 bps INFO @ Sat, 08 Aug 2020 12:49:36: #2 alternative fragment length(s) may be 193 bps INFO @ Sat, 08 Aug 2020 12:49:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392428/SRX8392428.10_model.r WARNING @ Sat, 08 Aug 2020 12:49:36: #2 Since the d (193) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:49:36: #2 You may need to consider one of the other alternative d(s): 193 WARNING @ Sat, 08 Aug 2020 12:49:36: #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 12:49:36: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:49:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:49:38: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:49:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392428/SRX8392428.10_peaks.xls INFO @ Sat, 08 Aug 2020 12:49:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392428/SRX8392428.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:49:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392428/SRX8392428.10_summits.bed INFO @ Sat, 08 Aug 2020 12:49:39: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (975 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 12:49:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8392428/SRX8392428.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8392428/SRX8392428.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8392428/SRX8392428.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8392428/SRX8392428.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 12:49:46: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:49:46: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:49:56: 1000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 12:50:06: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:50:06: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:50:06: #1 total tags in treatment: 760761 INFO @ Sat, 08 Aug 2020 12:50:06: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:50:06: #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 12:50:06: #1 tags after filtering in treatment: 729607 INFO @ Sat, 08 Aug 2020 12:50:06: #1 Redundant rate of treatment: 0.04 INFO @ Sat, 08 Aug 2020 12:50:06: #1 finished! INFO @ Sat, 08 Aug 2020 12:50:06: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:50:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:50:06: #2 number of paired peaks: 2858 INFO @ Sat, 08 Aug 2020 12:50:06: start model_add_line... INFO @ Sat, 08 Aug 2020 12:50:06: start X-correlation... INFO @ Sat, 08 Aug 2020 12:50:06: end of X-cor INFO @ Sat, 08 Aug 2020 12:50:06: #2 finished! INFO @ Sat, 08 Aug 2020 12:50:06: #2 predicted fragment length is 193 bps INFO @ Sat, 08 Aug 2020 12:50:06: #2 alternative fragment length(s) may be 193 bps INFO @ Sat, 08 Aug 2020 12:50:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8392428/SRX8392428.20_model.r WARNING @ Sat, 08 Aug 2020 12:50:06: #2 Since the d (193) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:50:06: #2 You may need to consider one of the other alternative d(s): 193 WARNING @ Sat, 08 Aug 2020 12:50:06: #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 12:50:06: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:50:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:50:08: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:50:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8392428/SRX8392428.20_peaks.xls INFO @ Sat, 08 Aug 2020 12:50:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8392428/SRX8392428.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:50:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8392428/SRX8392428.20_summits.bed INFO @ Sat, 08 Aug 2020 12:50:09: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (379 records, 4 fields): 2 millis CompletedMACS2peakCalling