Job ID = 14159575 SRX = SRX8845652 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 36116816 spots for SRR12345959/SRR12345959.sra Written 36116816 spots for SRR12345959/SRR12345959.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159949 ("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: 00:24:19 36116816 reads; of these: 36116816 (100.00%) were paired; of these: 15876987 (43.96%) aligned concordantly 0 times 17114955 (47.39%) aligned concordantly exactly 1 time 3124874 (8.65%) aligned concordantly >1 times ---- 15876987 pairs aligned concordantly 0 times; of these: 3159661 (19.90%) aligned discordantly 1 time ---- 12717326 pairs aligned 0 times concordantly or discordantly; of these: 25434652 mates make up the pairs; of these: 23185248 (91.16%) aligned 0 times 963143 (3.79%) aligned exactly 1 time 1286261 (5.06%) aligned >1 times 67.90% overall alignment rate Time searching: 00:24:19 Overall time: 00:24:19 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 20 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] 20617309 / 23190629 = 0.8890 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 23:12:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845652/SRX8845652.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845652/SRX8845652.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845652/SRX8845652.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845652/SRX8845652.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 23:12:57: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:12:57: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:13:03: 1000000 INFO @ Wed, 08 Dec 2021 23:13:08: 2000000 INFO @ Wed, 08 Dec 2021 23:13:14: 3000000 INFO @ Wed, 08 Dec 2021 23:13:20: 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 @ Wed, 08 Dec 2021 23:13:25: 5000000 INFO @ Wed, 08 Dec 2021 23:13:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845652/SRX8845652.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845652/SRX8845652.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845652/SRX8845652.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845652/SRX8845652.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 23:13:27: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:13:27: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:13:32: 6000000 INFO @ Wed, 08 Dec 2021 23:13:33: 1000000 INFO @ Wed, 08 Dec 2021 23:13:39: 7000000 INFO @ Wed, 08 Dec 2021 23:13:40: 2000000 INFO @ Wed, 08 Dec 2021 23:13:44: #1 tag size is determined as 73 bps INFO @ Wed, 08 Dec 2021 23:13:44: #1 tag size = 73 INFO @ Wed, 08 Dec 2021 23:13:44: #1 total tags in treatment: 2084747 INFO @ Wed, 08 Dec 2021 23:13:44: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:13:44: #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 23:13:44: #1 tags after filtering in treatment: 1364575 INFO @ Wed, 08 Dec 2021 23:13:44: #1 Redundant rate of treatment: 0.35 INFO @ Wed, 08 Dec 2021 23:13:44: #1 finished! INFO @ Wed, 08 Dec 2021 23:13:44: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:13:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:13:45: #2 number of paired peaks: 3638 INFO @ Wed, 08 Dec 2021 23:13:45: start model_add_line... INFO @ Wed, 08 Dec 2021 23:13:45: start X-correlation... INFO @ Wed, 08 Dec 2021 23:13:45: end of X-cor INFO @ Wed, 08 Dec 2021 23:13:45: #2 finished! INFO @ Wed, 08 Dec 2021 23:13:45: #2 predicted fragment length is 113 bps INFO @ Wed, 08 Dec 2021 23:13:45: #2 alternative fragment length(s) may be 113 bps INFO @ Wed, 08 Dec 2021 23:13:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845652/SRX8845652.05_model.r WARNING @ Wed, 08 Dec 2021 23:13:45: #2 Since the d (113) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:13:45: #2 You may need to consider one of the other alternative d(s): 113 WARNING @ Wed, 08 Dec 2021 23:13:45: #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 23:13:45: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:13:45: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:13:47: 3000000 INFO @ Wed, 08 Dec 2021 23:13:48: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:13:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845652/SRX8845652.05_peaks.xls INFO @ Wed, 08 Dec 2021 23:13:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845652/SRX8845652.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:13:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845652/SRX8845652.05_summits.bed INFO @ Wed, 08 Dec 2021 23:13:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4519 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:13:53: 4000000 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 23:13:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845652/SRX8845652.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845652/SRX8845652.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845652/SRX8845652.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845652/SRX8845652.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 23:13:57: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:13:57: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:13:59: 5000000 INFO @ Wed, 08 Dec 2021 23:14:04: 1000000 INFO @ Wed, 08 Dec 2021 23:14:06: 6000000 INFO @ Wed, 08 Dec 2021 23:14:10: 2000000 INFO @ Wed, 08 Dec 2021 23:14:13: 7000000 INFO @ Wed, 08 Dec 2021 23:14:17: 3000000 INFO @ Wed, 08 Dec 2021 23:14:19: #1 tag size is determined as 73 bps INFO @ Wed, 08 Dec 2021 23:14:19: #1 tag size = 73 INFO @ Wed, 08 Dec 2021 23:14:19: #1 total tags in treatment: 2084747 INFO @ Wed, 08 Dec 2021 23:14:19: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:14:19: #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 23:14:19: #1 tags after filtering in treatment: 1364575 INFO @ Wed, 08 Dec 2021 23:14:19: #1 Redundant rate of treatment: 0.35 INFO @ Wed, 08 Dec 2021 23:14:19: #1 finished! INFO @ Wed, 08 Dec 2021 23:14:19: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:14:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:14:19: #2 number of paired peaks: 3638 INFO @ Wed, 08 Dec 2021 23:14:19: start model_add_line... INFO @ Wed, 08 Dec 2021 23:14:19: start X-correlation... INFO @ Wed, 08 Dec 2021 23:14:19: end of X-cor INFO @ Wed, 08 Dec 2021 23:14:19: #2 finished! INFO @ Wed, 08 Dec 2021 23:14:19: #2 predicted fragment length is 113 bps INFO @ Wed, 08 Dec 2021 23:14:19: #2 alternative fragment length(s) may be 113 bps INFO @ Wed, 08 Dec 2021 23:14:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845652/SRX8845652.10_model.r WARNING @ Wed, 08 Dec 2021 23:14:19: #2 Since the d (113) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:14:19: #2 You may need to consider one of the other alternative d(s): 113 WARNING @ Wed, 08 Dec 2021 23:14:19: #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 23:14:19: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:14:19: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:14:22: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:14:24: 4000000 INFO @ Wed, 08 Dec 2021 23:14:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845652/SRX8845652.10_peaks.xls INFO @ Wed, 08 Dec 2021 23:14:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845652/SRX8845652.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:14:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845652/SRX8845652.10_summits.bed INFO @ Wed, 08 Dec 2021 23:14:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2591 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 23:14:30: 5000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 23:14:36: 6000000 INFO @ Wed, 08 Dec 2021 23:14:42: 7000000 INFO @ Wed, 08 Dec 2021 23:14:47: #1 tag size is determined as 73 bps INFO @ Wed, 08 Dec 2021 23:14:47: #1 tag size = 73 INFO @ Wed, 08 Dec 2021 23:14:47: #1 total tags in treatment: 2084747 INFO @ Wed, 08 Dec 2021 23:14:47: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:14:47: #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 23:14:47: #1 tags after filtering in treatment: 1364575 INFO @ Wed, 08 Dec 2021 23:14:47: #1 Redundant rate of treatment: 0.35 INFO @ Wed, 08 Dec 2021 23:14:47: #1 finished! INFO @ Wed, 08 Dec 2021 23:14:47: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:14:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:14:47: #2 number of paired peaks: 3638 INFO @ Wed, 08 Dec 2021 23:14:47: start model_add_line... INFO @ Wed, 08 Dec 2021 23:14:47: start X-correlation... INFO @ Wed, 08 Dec 2021 23:14:47: end of X-cor INFO @ Wed, 08 Dec 2021 23:14:47: #2 finished! INFO @ Wed, 08 Dec 2021 23:14:47: #2 predicted fragment length is 113 bps INFO @ Wed, 08 Dec 2021 23:14:47: #2 alternative fragment length(s) may be 113 bps INFO @ Wed, 08 Dec 2021 23:14:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845652/SRX8845652.20_model.r WARNING @ Wed, 08 Dec 2021 23:14:47: #2 Since the d (113) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:14:47: #2 You may need to consider one of the other alternative d(s): 113 WARNING @ Wed, 08 Dec 2021 23:14:47: #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 23:14:47: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:14:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:14:50: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:14:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845652/SRX8845652.20_peaks.xls INFO @ Wed, 08 Dec 2021 23:14:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845652/SRX8845652.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:14:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845652/SRX8845652.20_summits.bed INFO @ Wed, 08 Dec 2021 23:14:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1087 records, 4 fields): 2 millis CompletedMACS2peakCalling