Job ID = 14160303 SRX = SRX9567201 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14495034 spots for SRR13125176/SRR13125176.sra Written 14495034 spots for SRR13125176/SRR13125176.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160473 ("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: 00:27:48 14495034 reads; of these: 14495034 (100.00%) were paired; of these: 6473630 (44.66%) aligned concordantly 0 times 6989959 (48.22%) aligned concordantly exactly 1 time 1031445 (7.12%) aligned concordantly >1 times ---- 6473630 pairs aligned concordantly 0 times; of these: 4886224 (75.48%) aligned discordantly 1 time ---- 1587406 pairs aligned 0 times concordantly or discordantly; of these: 3174812 mates make up the pairs; of these: 1197320 (37.71%) aligned 0 times 905665 (28.53%) aligned exactly 1 time 1071827 (33.76%) aligned >1 times 95.87% overall alignment rate Time searching: 00:27:48 Overall time: 00:27:48 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 24 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] 8436763 / 12902740 = 0.6539 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 @ Thu, 09 Dec 2021 01:56:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567201/SRX9567201.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567201/SRX9567201.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567201/SRX9567201.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567201/SRX9567201.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 @ Thu, 09 Dec 2021 01:56:26: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:56:26: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:56:33: 1000000 INFO @ Thu, 09 Dec 2021 01:56:39: 2000000 INFO @ Thu, 09 Dec 2021 01:56:45: 3000000 INFO @ Thu, 09 Dec 2021 01:56:51: 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 @ Thu, 09 Dec 2021 01:56:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567201/SRX9567201.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567201/SRX9567201.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567201/SRX9567201.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567201/SRX9567201.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 @ Thu, 09 Dec 2021 01:56:56: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:56:56: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:56:58: 5000000 INFO @ Thu, 09 Dec 2021 01:57:03: 1000000 INFO @ Thu, 09 Dec 2021 01:57:04: 6000000 INFO @ Thu, 09 Dec 2021 01:57:10: 2000000 INFO @ Thu, 09 Dec 2021 01:57:11: 7000000 INFO @ Thu, 09 Dec 2021 01:57:17: 3000000 INFO @ Thu, 09 Dec 2021 01:57:18: 8000000 INFO @ Thu, 09 Dec 2021 01:57:25: 9000000 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 @ Thu, 09 Dec 2021 01:57:25: 4000000 INFO @ Thu, 09 Dec 2021 01:57:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567201/SRX9567201.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567201/SRX9567201.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567201/SRX9567201.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567201/SRX9567201.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 @ Thu, 09 Dec 2021 01:57:26: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:57:26: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:57:32: 10000000 INFO @ Thu, 09 Dec 2021 01:57:32: 5000000 INFO @ Thu, 09 Dec 2021 01:57:35: 1000000 INFO @ Thu, 09 Dec 2021 01:57:38: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 01:57:38: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 01:57:38: #1 total tags in treatment: 2812188 INFO @ Thu, 09 Dec 2021 01:57:38: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:57:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 01:57:38: #1 tags after filtering in treatment: 2608323 INFO @ Thu, 09 Dec 2021 01:57:38: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 09 Dec 2021 01:57:38: #1 finished! INFO @ Thu, 09 Dec 2021 01:57:38: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:57:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:57:38: #2 number of paired peaks: 2172 INFO @ Thu, 09 Dec 2021 01:57:38: start model_add_line... INFO @ Thu, 09 Dec 2021 01:57:38: start X-correlation... INFO @ Thu, 09 Dec 2021 01:57:38: end of X-cor INFO @ Thu, 09 Dec 2021 01:57:38: #2 finished! INFO @ Thu, 09 Dec 2021 01:57:38: #2 predicted fragment length is 276 bps INFO @ Thu, 09 Dec 2021 01:57:38: #2 alternative fragment length(s) may be 276 bps INFO @ Thu, 09 Dec 2021 01:57:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567201/SRX9567201.05_model.r WARNING @ Thu, 09 Dec 2021 01:57:38: #2 Since the d (276) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:57:38: #2 You may need to consider one of the other alternative d(s): 276 WARNING @ Thu, 09 Dec 2021 01:57:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 01:57:38: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:57:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:57:39: 6000000 INFO @ Thu, 09 Dec 2021 01:57:44: 2000000 INFO @ Thu, 09 Dec 2021 01:57:46: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:57:46: 7000000 INFO @ Thu, 09 Dec 2021 01:57:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567201/SRX9567201.05_peaks.xls INFO @ Thu, 09 Dec 2021 01:57:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567201/SRX9567201.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:57:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567201/SRX9567201.05_summits.bed INFO @ Thu, 09 Dec 2021 01:57:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1135 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 01:57:52: 3000000 INFO @ Thu, 09 Dec 2021 01:57:53: 8000000 INFO @ Thu, 09 Dec 2021 01:58:00: 9000000 INFO @ Thu, 09 Dec 2021 01:58:01: 4000000 INFO @ Thu, 09 Dec 2021 01:58:07: 10000000 INFO @ Thu, 09 Dec 2021 01:58:09: 5000000 INFO @ Thu, 09 Dec 2021 01:58:13: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 01:58:13: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 01:58:13: #1 total tags in treatment: 2812188 INFO @ Thu, 09 Dec 2021 01:58:13: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:58:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 01:58:13: #1 tags after filtering in treatment: 2608323 INFO @ Thu, 09 Dec 2021 01:58:13: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 09 Dec 2021 01:58:13: #1 finished! INFO @ Thu, 09 Dec 2021 01:58:13: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:58:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:58:13: #2 number of paired peaks: 2172 INFO @ Thu, 09 Dec 2021 01:58:13: start model_add_line... INFO @ Thu, 09 Dec 2021 01:58:13: start X-correlation... INFO @ Thu, 09 Dec 2021 01:58:13: end of X-cor INFO @ Thu, 09 Dec 2021 01:58:13: #2 finished! INFO @ Thu, 09 Dec 2021 01:58:13: #2 predicted fragment length is 276 bps INFO @ Thu, 09 Dec 2021 01:58:13: #2 alternative fragment length(s) may be 276 bps INFO @ Thu, 09 Dec 2021 01:58:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567201/SRX9567201.10_model.r WARNING @ Thu, 09 Dec 2021 01:58:13: #2 Since the d (276) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:58:13: #2 You may need to consider one of the other alternative d(s): 276 WARNING @ Thu, 09 Dec 2021 01:58:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 01:58:13: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:58:13: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:58:17: 6000000 INFO @ Thu, 09 Dec 2021 01:58:21: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 01:58:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567201/SRX9567201.10_peaks.xls INFO @ Thu, 09 Dec 2021 01:58:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567201/SRX9567201.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:58:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567201/SRX9567201.10_summits.bed INFO @ Thu, 09 Dec 2021 01:58:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (633 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 01:58:26: 7000000 INFO @ Thu, 09 Dec 2021 01:58:34: 8000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 01:58:42: 9000000 INFO @ Thu, 09 Dec 2021 01:58:50: 10000000 INFO @ Thu, 09 Dec 2021 01:58:57: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 01:58:57: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 01:58:57: #1 total tags in treatment: 2812188 INFO @ Thu, 09 Dec 2021 01:58:57: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:58:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 01:58:58: #1 tags after filtering in treatment: 2608323 INFO @ Thu, 09 Dec 2021 01:58:58: #1 Redundant rate of treatment: 0.07 INFO @ Thu, 09 Dec 2021 01:58:58: #1 finished! INFO @ Thu, 09 Dec 2021 01:58:58: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:58:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:58:58: #2 number of paired peaks: 2172 INFO @ Thu, 09 Dec 2021 01:58:58: start model_add_line... INFO @ Thu, 09 Dec 2021 01:58:58: start X-correlation... INFO @ Thu, 09 Dec 2021 01:58:58: end of X-cor INFO @ Thu, 09 Dec 2021 01:58:58: #2 finished! INFO @ Thu, 09 Dec 2021 01:58:58: #2 predicted fragment length is 276 bps INFO @ Thu, 09 Dec 2021 01:58:58: #2 alternative fragment length(s) may be 276 bps INFO @ Thu, 09 Dec 2021 01:58:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567201/SRX9567201.20_model.r WARNING @ Thu, 09 Dec 2021 01:58:58: #2 Since the d (276) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 01:58:58: #2 You may need to consider one of the other alternative d(s): 276 WARNING @ Thu, 09 Dec 2021 01:58:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 01:58:58: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:58:58: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:59:05: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:59:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567201/SRX9567201.20_peaks.xls INFO @ Thu, 09 Dec 2021 01:59:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567201/SRX9567201.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:59:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567201/SRX9567201.20_summits.bed INFO @ Thu, 09 Dec 2021 01:59:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (329 records, 4 fields): 1 millis CompletedMACS2peakCalling