Job ID = 14159515 SRX = SRX8845629 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10128985 spots for SRR12345974/SRR12345974.sra Written 10128985 spots for SRR12345974/SRR12345974.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159695 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:16 10128985 reads; of these: 10128985 (100.00%) were paired; of these: 2590232 (25.57%) aligned concordantly 0 times 6779603 (66.93%) aligned concordantly exactly 1 time 759150 (7.49%) aligned concordantly >1 times ---- 2590232 pairs aligned concordantly 0 times; of these: 1215332 (46.92%) aligned discordantly 1 time ---- 1374900 pairs aligned 0 times concordantly or discordantly; of these: 2749800 mates make up the pairs; of these: 2221208 (80.78%) aligned 0 times 275351 (10.01%) aligned exactly 1 time 253241 (9.21%) aligned >1 times 89.04% overall alignment rate Time searching: 00:09:16 Overall time: 00:09:16 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] 6363646 / 8679073 = 0.7332 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 22:31:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845629/SRX8845629.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845629/SRX8845629.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845629/SRX8845629.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845629/SRX8845629.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 22:31:15: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:31:15: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:31:21: 1000000 INFO @ Wed, 08 Dec 2021 22:31:26: 2000000 INFO @ Wed, 08 Dec 2021 22:31:32: 3000000 INFO @ Wed, 08 Dec 2021 22:31:37: 4000000 INFO @ Wed, 08 Dec 2021 22:31:42: 5000000 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 22:31:44: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 22:31:44: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 22:31:44: #1 total tags in treatment: 1925236 INFO @ Wed, 08 Dec 2021 22:31:44: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:31:44: #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 22:31:44: #1 tags after filtering in treatment: 1427957 INFO @ Wed, 08 Dec 2021 22:31:44: #1 Redundant rate of treatment: 0.26 INFO @ Wed, 08 Dec 2021 22:31:44: #1 finished! INFO @ Wed, 08 Dec 2021 22:31:44: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:31:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:31:44: #2 number of paired peaks: 4264 INFO @ Wed, 08 Dec 2021 22:31:44: start model_add_line... INFO @ Wed, 08 Dec 2021 22:31:44: start X-correlation... INFO @ Wed, 08 Dec 2021 22:31:44: end of X-cor INFO @ Wed, 08 Dec 2021 22:31:44: #2 finished! INFO @ Wed, 08 Dec 2021 22:31:44: #2 predicted fragment length is 119 bps INFO @ Wed, 08 Dec 2021 22:31:44: #2 alternative fragment length(s) may be 119 bps INFO @ Wed, 08 Dec 2021 22:31:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845629/SRX8845629.05_model.r WARNING @ Wed, 08 Dec 2021 22:31:44: #2 Since the d (119) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:31:44: #2 You may need to consider one of the other alternative d(s): 119 WARNING @ Wed, 08 Dec 2021 22:31:44: #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 22:31:44: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:31:44: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:31:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845629/SRX8845629.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845629/SRX8845629.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845629/SRX8845629.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845629/SRX8845629.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 22:31:45: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:31:45: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:31:48: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:31:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845629/SRX8845629.05_peaks.xls INFO @ Wed, 08 Dec 2021 22:31:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845629/SRX8845629.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:31:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845629/SRX8845629.05_summits.bed INFO @ Wed, 08 Dec 2021 22:31:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5657 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:31:51: 1000000 INFO @ Wed, 08 Dec 2021 22:31:57: 2000000 INFO @ Wed, 08 Dec 2021 22:32:02: 3000000 INFO @ Wed, 08 Dec 2021 22:32:08: 4000000 INFO @ Wed, 08 Dec 2021 22:32:13: 5000000 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 22:32:15: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 22:32:15: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 22:32:15: #1 total tags in treatment: 1925236 INFO @ Wed, 08 Dec 2021 22:32:15: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:32:15: #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 22:32:15: #1 tags after filtering in treatment: 1427957 INFO @ Wed, 08 Dec 2021 22:32:15: #1 Redundant rate of treatment: 0.26 INFO @ Wed, 08 Dec 2021 22:32:15: #1 finished! INFO @ Wed, 08 Dec 2021 22:32:15: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:32:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:32:15: #2 number of paired peaks: 4264 INFO @ Wed, 08 Dec 2021 22:32:15: start model_add_line... INFO @ Wed, 08 Dec 2021 22:32:15: start X-correlation... INFO @ Wed, 08 Dec 2021 22:32:15: end of X-cor INFO @ Wed, 08 Dec 2021 22:32:15: #2 finished! INFO @ Wed, 08 Dec 2021 22:32:15: #2 predicted fragment length is 119 bps INFO @ Wed, 08 Dec 2021 22:32:15: #2 alternative fragment length(s) may be 119 bps INFO @ Wed, 08 Dec 2021 22:32:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845629/SRX8845629.10_model.r WARNING @ Wed, 08 Dec 2021 22:32:15: #2 Since the d (119) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:32:15: #2 You may need to consider one of the other alternative d(s): 119 WARNING @ Wed, 08 Dec 2021 22:32:15: #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 22:32:15: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:32:15: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:32:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845629/SRX8845629.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845629/SRX8845629.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845629/SRX8845629.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845629/SRX8845629.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 22:32:15: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:32:15: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:32:19: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:32:20: 1000000 INFO @ Wed, 08 Dec 2021 22:32:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845629/SRX8845629.10_peaks.xls INFO @ Wed, 08 Dec 2021 22:32:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845629/SRX8845629.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:32:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845629/SRX8845629.10_summits.bed INFO @ Wed, 08 Dec 2021 22:32:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3341 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:32:25: 2000000 INFO @ Wed, 08 Dec 2021 22:32:30: 3000000 INFO @ Wed, 08 Dec 2021 22:32:35: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 22:32:40: 5000000 INFO @ Wed, 08 Dec 2021 22:32:41: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 22:32:41: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 22:32:41: #1 total tags in treatment: 1925236 INFO @ Wed, 08 Dec 2021 22:32:41: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:32:41: #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 22:32:41: #1 tags after filtering in treatment: 1427957 INFO @ Wed, 08 Dec 2021 22:32:41: #1 Redundant rate of treatment: 0.26 INFO @ Wed, 08 Dec 2021 22:32:41: #1 finished! INFO @ Wed, 08 Dec 2021 22:32:41: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:32:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:32:42: #2 number of paired peaks: 4264 INFO @ Wed, 08 Dec 2021 22:32:42: start model_add_line... INFO @ Wed, 08 Dec 2021 22:32:42: start X-correlation... INFO @ Wed, 08 Dec 2021 22:32:42: end of X-cor INFO @ Wed, 08 Dec 2021 22:32:42: #2 finished! INFO @ Wed, 08 Dec 2021 22:32:42: #2 predicted fragment length is 119 bps INFO @ Wed, 08 Dec 2021 22:32:42: #2 alternative fragment length(s) may be 119 bps INFO @ Wed, 08 Dec 2021 22:32:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845629/SRX8845629.20_model.r WARNING @ Wed, 08 Dec 2021 22:32:42: #2 Since the d (119) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:32:42: #2 You may need to consider one of the other alternative d(s): 119 WARNING @ Wed, 08 Dec 2021 22:32:42: #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 22:32:42: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:32:42: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 22:32:45: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:32:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845629/SRX8845629.20_peaks.xls INFO @ Wed, 08 Dec 2021 22:32:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845629/SRX8845629.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:32:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845629/SRX8845629.20_summits.bed INFO @ Wed, 08 Dec 2021 22:32:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1682 records, 4 fields): 3 millis CompletedMACS2peakCalling