Job ID = 14158397 SRX = SRX10641187 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-08T08:21:21 prefetch.2.10.7: 1) Downloading 'SRR14280091'... 2021-12-08T08:21:21 prefetch.2.10.7: Downloading via HTTPS... 2021-12-08T08:33:54 prefetch.2.10.7: HTTPS download succeed 2021-12-08T08:33:54 prefetch.2.10.7: 1) 'SRR14280091' was downloaded successfully 2021-12-08T08:33:54 prefetch.2.10.7: 'SRR14280091' has 0 unresolved dependencies Read 21335755 spots for SRR14280091/SRR14280091.sra Written 21335755 spots for SRR14280091/SRR14280091.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159139 ("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: 00:15:39 21335755 reads; of these: 21335755 (100.00%) were paired; of these: 16954442 (79.46%) aligned concordantly 0 times 3855916 (18.07%) aligned concordantly exactly 1 time 525397 (2.46%) aligned concordantly >1 times ---- 16954442 pairs aligned concordantly 0 times; of these: 1969545 (11.62%) aligned discordantly 1 time ---- 14984897 pairs aligned 0 times concordantly or discordantly; of these: 29969794 mates make up the pairs; of these: 29007213 (96.79%) aligned 0 times 563129 (1.88%) aligned exactly 1 time 399452 (1.33%) aligned >1 times 32.02% overall alignment rate Time searching: 00:15:39 Overall time: 00:15:39 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] 832087 / 6327937 = 0.1315 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 17:58:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641187/SRX10641187.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641187/SRX10641187.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641187/SRX10641187.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641187/SRX10641187.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 17:58:59: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:58:59: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:59:09: 1000000 INFO @ Wed, 08 Dec 2021 17:59:19: 2000000 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 17:59:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641187/SRX10641187.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641187/SRX10641187.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641187/SRX10641187.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641187/SRX10641187.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 17:59:29: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:59:29: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:59:29: 3000000 INFO @ Wed, 08 Dec 2021 17:59:39: 4000000 INFO @ Wed, 08 Dec 2021 17:59:40: 1000000 INFO @ Wed, 08 Dec 2021 17:59:49: 5000000 INFO @ Wed, 08 Dec 2021 17:59:50: 2000000 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 17:59:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641187/SRX10641187.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641187/SRX10641187.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641187/SRX10641187.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641187/SRX10641187.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 17:59:58: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:59:58: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:59:59: 6000000 INFO @ Wed, 08 Dec 2021 18:00:01: 3000000 INFO @ Wed, 08 Dec 2021 18:00:08: 1000000 INFO @ Wed, 08 Dec 2021 18:00:10: 7000000 INFO @ Wed, 08 Dec 2021 18:00:12: 4000000 INFO @ Wed, 08 Dec 2021 18:00:17: 2000000 INFO @ Wed, 08 Dec 2021 18:00:20: 8000000 INFO @ Wed, 08 Dec 2021 18:00:23: 5000000 INFO @ Wed, 08 Dec 2021 18:00:27: 3000000 INFO @ Wed, 08 Dec 2021 18:00:31: 9000000 INFO @ Wed, 08 Dec 2021 18:00:33: 6000000 INFO @ Wed, 08 Dec 2021 18:00:36: 4000000 INFO @ Wed, 08 Dec 2021 18:00:41: 10000000 INFO @ Wed, 08 Dec 2021 18:00:44: 7000000 INFO @ Wed, 08 Dec 2021 18:00:45: 5000000 INFO @ Wed, 08 Dec 2021 18:00:51: 11000000 INFO @ Wed, 08 Dec 2021 18:00:55: 6000000 INFO @ Wed, 08 Dec 2021 18:00:55: 8000000 INFO @ Wed, 08 Dec 2021 18:01:02: 12000000 INFO @ Wed, 08 Dec 2021 18:01:02: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 18:01:02: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 18:01:02: #1 total tags in treatment: 3747501 INFO @ Wed, 08 Dec 2021 18:01:02: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:01:02: #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 18:01:02: #1 tags after filtering in treatment: 3527750 INFO @ Wed, 08 Dec 2021 18:01:02: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 18:01:02: #1 finished! INFO @ Wed, 08 Dec 2021 18:01:02: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:01:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:01:02: #2 number of paired peaks: 1142 INFO @ Wed, 08 Dec 2021 18:01:02: start model_add_line... INFO @ Wed, 08 Dec 2021 18:01:02: start X-correlation... INFO @ Wed, 08 Dec 2021 18:01:02: end of X-cor INFO @ Wed, 08 Dec 2021 18:01:02: #2 finished! INFO @ Wed, 08 Dec 2021 18:01:02: #2 predicted fragment length is 237 bps INFO @ Wed, 08 Dec 2021 18:01:02: #2 alternative fragment length(s) may be 237 bps INFO @ Wed, 08 Dec 2021 18:01:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641187/SRX10641187.05_model.r WARNING @ Wed, 08 Dec 2021 18:01:02: #2 Since the d (237) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:01:02: #2 You may need to consider one of the other alternative d(s): 237 WARNING @ Wed, 08 Dec 2021 18:01:02: #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 18:01:02: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:01:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:01:04: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:01:06: 9000000 INFO @ Wed, 08 Dec 2021 18:01:11: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:01:13: 8000000 INFO @ Wed, 08 Dec 2021 18:01:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641187/SRX10641187.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:01:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641187/SRX10641187.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:01:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641187/SRX10641187.05_summits.bed INFO @ Wed, 08 Dec 2021 18:01:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1395 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:01:16: 10000000 INFO @ Wed, 08 Dec 2021 18:01:22: 9000000 INFO @ Wed, 08 Dec 2021 18:01:27: 11000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:01:31: 10000000 INFO @ Wed, 08 Dec 2021 18:01:37: 12000000 INFO @ Wed, 08 Dec 2021 18:01:37: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 18:01:37: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 18:01:37: #1 total tags in treatment: 3747501 INFO @ Wed, 08 Dec 2021 18:01:37: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:01:37: #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 18:01:37: #1 tags after filtering in treatment: 3527750 INFO @ Wed, 08 Dec 2021 18:01:37: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 18:01:37: #1 finished! INFO @ Wed, 08 Dec 2021 18:01:37: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:01:37: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:01:38: #2 number of paired peaks: 1142 INFO @ Wed, 08 Dec 2021 18:01:38: start model_add_line... INFO @ Wed, 08 Dec 2021 18:01:38: start X-correlation... INFO @ Wed, 08 Dec 2021 18:01:38: end of X-cor INFO @ Wed, 08 Dec 2021 18:01:38: #2 finished! INFO @ Wed, 08 Dec 2021 18:01:38: #2 predicted fragment length is 237 bps INFO @ Wed, 08 Dec 2021 18:01:38: #2 alternative fragment length(s) may be 237 bps INFO @ Wed, 08 Dec 2021 18:01:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641187/SRX10641187.10_model.r WARNING @ Wed, 08 Dec 2021 18:01:38: #2 Since the d (237) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:01:38: #2 You may need to consider one of the other alternative d(s): 237 WARNING @ Wed, 08 Dec 2021 18:01:38: #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 18:01:38: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:01:38: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:01:40: 11000000 INFO @ Wed, 08 Dec 2021 18:01:48: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:01:48: 12000000 INFO @ Wed, 08 Dec 2021 18:01:48: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 18:01:48: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 18:01:48: #1 total tags in treatment: 3747501 INFO @ Wed, 08 Dec 2021 18:01:48: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:01:48: #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 18:01:48: #1 tags after filtering in treatment: 3527750 INFO @ Wed, 08 Dec 2021 18:01:48: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 18:01:48: #1 finished! INFO @ Wed, 08 Dec 2021 18:01:48: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:01:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:01:48: #2 number of paired peaks: 1142 INFO @ Wed, 08 Dec 2021 18:01:48: start model_add_line... INFO @ Wed, 08 Dec 2021 18:01:48: start X-correlation... INFO @ Wed, 08 Dec 2021 18:01:48: end of X-cor INFO @ Wed, 08 Dec 2021 18:01:48: #2 finished! INFO @ Wed, 08 Dec 2021 18:01:48: #2 predicted fragment length is 237 bps INFO @ Wed, 08 Dec 2021 18:01:48: #2 alternative fragment length(s) may be 237 bps INFO @ Wed, 08 Dec 2021 18:01:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641187/SRX10641187.20_model.r WARNING @ Wed, 08 Dec 2021 18:01:48: #2 Since the d (237) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:01:48: #2 You may need to consider one of the other alternative d(s): 237 WARNING @ Wed, 08 Dec 2021 18:01:48: #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 18:01:48: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:01:48: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:01:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641187/SRX10641187.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:01:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641187/SRX10641187.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:01:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641187/SRX10641187.10_summits.bed INFO @ Wed, 08 Dec 2021 18:01:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (565 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:01:57: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:02:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641187/SRX10641187.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:02:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641187/SRX10641187.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:02:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641187/SRX10641187.20_summits.bed INFO @ Wed, 08 Dec 2021 18:02:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (256 records, 4 fields): 25 millis CompletedMACS2peakCalling