Job ID = 14157932 SRX = SRX10641202 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 21797330 spots for SRR14280076/SRR14280076.sra Written 21797330 spots for SRR14280076/SRR14280076.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158217 ("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: 00:34:13 21797330 reads; of these: 21797330 (100.00%) were paired; of these: 15096679 (69.26%) aligned concordantly 0 times 3628624 (16.65%) aligned concordantly exactly 1 time 3072027 (14.09%) aligned concordantly >1 times ---- 15096679 pairs aligned concordantly 0 times; of these: 1846205 (12.23%) aligned discordantly 1 time ---- 13250474 pairs aligned 0 times concordantly or discordantly; of these: 26500948 mates make up the pairs; of these: 25325131 (95.56%) aligned 0 times 564848 (2.13%) aligned exactly 1 time 610969 (2.31%) aligned >1 times 41.91% overall alignment rate Time searching: 00:34:13 Overall time: 00:34:13 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 16 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] 2116643 / 8512509 = 0.2487 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 13:38:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641202/SRX10641202.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641202/SRX10641202.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641202/SRX10641202.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641202/SRX10641202.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 13:38:30: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:38:30: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:38:40: 1000000 INFO @ Wed, 08 Dec 2021 13:38:50: 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 13:39:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641202/SRX10641202.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641202/SRX10641202.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641202/SRX10641202.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641202/SRX10641202.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 13:39:00: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:39:00: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:39:01: 3000000 INFO @ Wed, 08 Dec 2021 13:39:09: 1000000 INFO @ Wed, 08 Dec 2021 13:39:12: 4000000 INFO @ Wed, 08 Dec 2021 13:39:19: 2000000 INFO @ Wed, 08 Dec 2021 13:39:23: 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 13:39:29: 3000000 INFO @ Wed, 08 Dec 2021 13:39:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641202/SRX10641202.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641202/SRX10641202.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641202/SRX10641202.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641202/SRX10641202.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 13:39:30: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:39:30: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:39:33: 6000000 INFO @ Wed, 08 Dec 2021 13:39:38: 4000000 INFO @ Wed, 08 Dec 2021 13:39:41: 1000000 INFO @ Wed, 08 Dec 2021 13:39:44: 7000000 INFO @ Wed, 08 Dec 2021 13:39:48: 5000000 INFO @ Wed, 08 Dec 2021 13:39:53: 2000000 INFO @ Wed, 08 Dec 2021 13:39:54: 8000000 INFO @ Wed, 08 Dec 2021 13:39:58: 6000000 INFO @ Wed, 08 Dec 2021 13:40:04: 3000000 INFO @ Wed, 08 Dec 2021 13:40:05: 9000000 INFO @ Wed, 08 Dec 2021 13:40:08: 7000000 INFO @ Wed, 08 Dec 2021 13:40:15: 4000000 INFO @ Wed, 08 Dec 2021 13:40:16: 10000000 INFO @ Wed, 08 Dec 2021 13:40:17: 8000000 INFO @ Wed, 08 Dec 2021 13:40:26: 5000000 INFO @ Wed, 08 Dec 2021 13:40:26: 11000000 INFO @ Wed, 08 Dec 2021 13:40:27: 9000000 INFO @ Wed, 08 Dec 2021 13:40:36: 10000000 INFO @ Wed, 08 Dec 2021 13:40:37: 12000000 INFO @ Wed, 08 Dec 2021 13:40:37: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 13:40:46: 11000000 INFO @ Wed, 08 Dec 2021 13:40:48: 13000000 INFO @ Wed, 08 Dec 2021 13:40:48: 7000000 INFO @ Wed, 08 Dec 2021 13:40:55: 12000000 INFO @ Wed, 08 Dec 2021 13:40:59: 8000000 INFO @ Wed, 08 Dec 2021 13:40:59: 14000000 INFO @ Wed, 08 Dec 2021 13:40:59: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 13:40:59: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 13:40:59: #1 total tags in treatment: 4832078 INFO @ Wed, 08 Dec 2021 13:40:59: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 13:40:59: #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 13:40:59: #1 tags after filtering in treatment: 3437273 INFO @ Wed, 08 Dec 2021 13:40:59: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 08 Dec 2021 13:40:59: #1 finished! INFO @ Wed, 08 Dec 2021 13:40:59: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 13:40:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 13:40:59: #2 number of paired peaks: 1076 INFO @ Wed, 08 Dec 2021 13:40:59: start model_add_line... INFO @ Wed, 08 Dec 2021 13:40:59: start X-correlation... INFO @ Wed, 08 Dec 2021 13:40:59: end of X-cor INFO @ Wed, 08 Dec 2021 13:40:59: #2 finished! INFO @ Wed, 08 Dec 2021 13:40:59: #2 predicted fragment length is 279 bps INFO @ Wed, 08 Dec 2021 13:40:59: #2 alternative fragment length(s) may be 279 bps INFO @ Wed, 08 Dec 2021 13:40:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641202/SRX10641202.05_model.r WARNING @ Wed, 08 Dec 2021 13:40:59: #2 Since the d (279) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 13:40:59: #2 You may need to consider one of the other alternative d(s): 279 WARNING @ Wed, 08 Dec 2021 13:40:59: #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 13:40:59: #3 Call peaks... INFO @ Wed, 08 Dec 2021 13:40:59: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 13:41:05: 13000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 13:41:09: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 13:41:09: 9000000 INFO @ Wed, 08 Dec 2021 13:41:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641202/SRX10641202.05_peaks.xls INFO @ Wed, 08 Dec 2021 13:41:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641202/SRX10641202.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 13:41:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641202/SRX10641202.05_summits.bed INFO @ Wed, 08 Dec 2021 13:41:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (829 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 13:41:14: 14000000 INFO @ Wed, 08 Dec 2021 13:41:14: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 13:41:14: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 13:41:14: #1 total tags in treatment: 4832078 INFO @ Wed, 08 Dec 2021 13:41:14: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 13:41:14: #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 13:41:14: #1 tags after filtering in treatment: 3437273 INFO @ Wed, 08 Dec 2021 13:41:14: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 08 Dec 2021 13:41:14: #1 finished! INFO @ Wed, 08 Dec 2021 13:41:14: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 13:41:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 13:41:15: #2 number of paired peaks: 1076 INFO @ Wed, 08 Dec 2021 13:41:15: start model_add_line... INFO @ Wed, 08 Dec 2021 13:41:15: start X-correlation... INFO @ Wed, 08 Dec 2021 13:41:15: end of X-cor INFO @ Wed, 08 Dec 2021 13:41:15: #2 finished! INFO @ Wed, 08 Dec 2021 13:41:15: #2 predicted fragment length is 279 bps INFO @ Wed, 08 Dec 2021 13:41:15: #2 alternative fragment length(s) may be 279 bps INFO @ Wed, 08 Dec 2021 13:41:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641202/SRX10641202.10_model.r WARNING @ Wed, 08 Dec 2021 13:41:15: #2 Since the d (279) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 13:41:15: #2 You may need to consider one of the other alternative d(s): 279 WARNING @ Wed, 08 Dec 2021 13:41:15: #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 13:41:15: #3 Call peaks... INFO @ Wed, 08 Dec 2021 13:41:15: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 13:41:19: 10000000 INFO @ Wed, 08 Dec 2021 13:41:25: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 13:41:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641202/SRX10641202.10_peaks.xls INFO @ Wed, 08 Dec 2021 13:41:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641202/SRX10641202.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 13:41:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641202/SRX10641202.10_summits.bed INFO @ Wed, 08 Dec 2021 13:41:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (641 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 13:41:29: 11000000 INFO @ Wed, 08 Dec 2021 13:41:39: 12000000 INFO @ Wed, 08 Dec 2021 13:41:49: 13000000 INFO @ Wed, 08 Dec 2021 13:41:58: 14000000 INFO @ Wed, 08 Dec 2021 13:41:59: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 13:41:59: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 13:41:59: #1 total tags in treatment: 4832078 INFO @ Wed, 08 Dec 2021 13:41:59: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 13:41:59: #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 13:41:59: #1 tags after filtering in treatment: 3437273 INFO @ Wed, 08 Dec 2021 13:41:59: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 08 Dec 2021 13:41:59: #1 finished! INFO @ Wed, 08 Dec 2021 13:41:59: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 13:41:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 13:41:59: #2 number of paired peaks: 1076 INFO @ Wed, 08 Dec 2021 13:41:59: start model_add_line... INFO @ Wed, 08 Dec 2021 13:41:59: start X-correlation... INFO @ Wed, 08 Dec 2021 13:41:59: end of X-cor INFO @ Wed, 08 Dec 2021 13:41:59: #2 finished! INFO @ Wed, 08 Dec 2021 13:41:59: #2 predicted fragment length is 279 bps INFO @ Wed, 08 Dec 2021 13:41:59: #2 alternative fragment length(s) may be 279 bps INFO @ Wed, 08 Dec 2021 13:41:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641202/SRX10641202.20_model.r WARNING @ Wed, 08 Dec 2021 13:41:59: #2 Since the d (279) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 13:41:59: #2 You may need to consider one of the other alternative d(s): 279 WARNING @ Wed, 08 Dec 2021 13:41:59: #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 13:41:59: #3 Call peaks... INFO @ Wed, 08 Dec 2021 13:41:59: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 13:42:09: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 13:42:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641202/SRX10641202.20_peaks.xls INFO @ Wed, 08 Dec 2021 13:42:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641202/SRX10641202.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 13:42:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641202/SRX10641202.20_summits.bed INFO @ Wed, 08 Dec 2021 13:42:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (484 records, 4 fields): 1 millis CompletedMACS2peakCalling