Job ID = 14159547 SRX = SRX8845643 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 34620754 spots for SRR12345950/SRR12345950.sra Written 34620754 spots for SRR12345950/SRR12345950.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159950 ("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: 00:37:55 34620754 reads; of these: 34620754 (100.00%) were paired; of these: 20032232 (57.86%) aligned concordantly 0 times 12490481 (36.08%) aligned concordantly exactly 1 time 2098041 (6.06%) aligned concordantly >1 times ---- 20032232 pairs aligned concordantly 0 times; of these: 2001635 (9.99%) aligned discordantly 1 time ---- 18030597 pairs aligned 0 times concordantly or discordantly; of these: 36061194 mates make up the pairs; of these: 34718232 (96.28%) aligned 0 times 374262 (1.04%) aligned exactly 1 time 968700 (2.69%) aligned >1 times 49.86% overall alignment rate Time searching: 00:37:55 Overall time: 00:37:55 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] 3058713 / 16526617 = 0.1851 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 23:14:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845643/SRX8845643.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845643/SRX8845643.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845643/SRX8845643.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845643/SRX8845643.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 23:14:47: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:14:47: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:14:55: 1000000 INFO @ Wed, 08 Dec 2021 23:15:02: 2000000 INFO @ Wed, 08 Dec 2021 23:15:09: 3000000 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 23:15:16: 4000000 INFO @ Wed, 08 Dec 2021 23:15:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845643/SRX8845643.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845643/SRX8845643.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845643/SRX8845643.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845643/SRX8845643.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 23:15:17: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:15:17: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:15:23: 1000000 INFO @ Wed, 08 Dec 2021 23:15:23: 5000000 INFO @ Wed, 08 Dec 2021 23:15:29: 2000000 INFO @ Wed, 08 Dec 2021 23:15:31: 6000000 INFO @ Wed, 08 Dec 2021 23:15:35: 3000000 INFO @ Wed, 08 Dec 2021 23:15:38: 7000000 INFO @ Wed, 08 Dec 2021 23:15:41: 4000000 INFO @ Wed, 08 Dec 2021 23:15:45: 8000000 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 23:15:47: 5000000 INFO @ Wed, 08 Dec 2021 23:15:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845643/SRX8845643.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845643/SRX8845643.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845643/SRX8845643.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845643/SRX8845643.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 23:15:47: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:15:47: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:15:53: 9000000 INFO @ Wed, 08 Dec 2021 23:15:53: 6000000 INFO @ Wed, 08 Dec 2021 23:15:54: 1000000 INFO @ Wed, 08 Dec 2021 23:15:59: 7000000 INFO @ Wed, 08 Dec 2021 23:16:00: 10000000 INFO @ Wed, 08 Dec 2021 23:16:01: 2000000 INFO @ Wed, 08 Dec 2021 23:16:05: 8000000 INFO @ Wed, 08 Dec 2021 23:16:08: 11000000 INFO @ Wed, 08 Dec 2021 23:16:09: 3000000 INFO @ Wed, 08 Dec 2021 23:16:11: 9000000 INFO @ Wed, 08 Dec 2021 23:16:15: 12000000 INFO @ Wed, 08 Dec 2021 23:16:16: 4000000 INFO @ Wed, 08 Dec 2021 23:16:17: 10000000 INFO @ Wed, 08 Dec 2021 23:16:22: 13000000 INFO @ Wed, 08 Dec 2021 23:16:23: 11000000 INFO @ Wed, 08 Dec 2021 23:16:23: 5000000 INFO @ Wed, 08 Dec 2021 23:16:29: 12000000 INFO @ Wed, 08 Dec 2021 23:16:30: 14000000 INFO @ Wed, 08 Dec 2021 23:16:31: 6000000 INFO @ Wed, 08 Dec 2021 23:16:35: 13000000 INFO @ Wed, 08 Dec 2021 23:16:37: 15000000 INFO @ Wed, 08 Dec 2021 23:16:38: 7000000 INFO @ Wed, 08 Dec 2021 23:16:41: 14000000 INFO @ Wed, 08 Dec 2021 23:16:44: 16000000 INFO @ Wed, 08 Dec 2021 23:16:46: 8000000 INFO @ Wed, 08 Dec 2021 23:16:47: 15000000 INFO @ Wed, 08 Dec 2021 23:16:52: 17000000 INFO @ Wed, 08 Dec 2021 23:16:53: 9000000 INFO @ Wed, 08 Dec 2021 23:16:53: 16000000 INFO @ Wed, 08 Dec 2021 23:16:59: 18000000 INFO @ Wed, 08 Dec 2021 23:17:00: 17000000 INFO @ Wed, 08 Dec 2021 23:17:00: 10000000 INFO @ Wed, 08 Dec 2021 23:17:06: 18000000 INFO @ Wed, 08 Dec 2021 23:17:07: 19000000 INFO @ Wed, 08 Dec 2021 23:17:08: 11000000 INFO @ Wed, 08 Dec 2021 23:17:12: 19000000 INFO @ Wed, 08 Dec 2021 23:17:14: 20000000 INFO @ Wed, 08 Dec 2021 23:17:15: 12000000 INFO @ Wed, 08 Dec 2021 23:17:18: 20000000 INFO @ Wed, 08 Dec 2021 23:17:22: 21000000 INFO @ Wed, 08 Dec 2021 23:17:23: 13000000 INFO @ Wed, 08 Dec 2021 23:17:25: 21000000 INFO @ Wed, 08 Dec 2021 23:17:28: 22000000 INFO @ Wed, 08 Dec 2021 23:17:30: 14000000 INFO @ Wed, 08 Dec 2021 23:17:31: 22000000 INFO @ Wed, 08 Dec 2021 23:17:35: 23000000 INFO @ Wed, 08 Dec 2021 23:17:36: 23000000 INFO @ Wed, 08 Dec 2021 23:17:38: 15000000 INFO @ Wed, 08 Dec 2021 23:17:42: 24000000 INFO @ Wed, 08 Dec 2021 23:17:43: 24000000 INFO @ Wed, 08 Dec 2021 23:17:46: 16000000 INFO @ Wed, 08 Dec 2021 23:17:49: 25000000 INFO @ Wed, 08 Dec 2021 23:17:50: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 23:17:53: 17000000 INFO @ Wed, 08 Dec 2021 23:17:56: 26000000 INFO @ Wed, 08 Dec 2021 23:17:57: 26000000 INFO @ Wed, 08 Dec 2021 23:18:01: 18000000 INFO @ Wed, 08 Dec 2021 23:18:03: 27000000 INFO @ Wed, 08 Dec 2021 23:18:04: 27000000 INFO @ Wed, 08 Dec 2021 23:18:09: 19000000 INFO @ Wed, 08 Dec 2021 23:18:10: 28000000 INFO @ Wed, 08 Dec 2021 23:18:11: 28000000 INFO @ Wed, 08 Dec 2021 23:18:14: #1 tag size is determined as 125 bps INFO @ Wed, 08 Dec 2021 23:18:14: #1 tag size = 125 INFO @ Wed, 08 Dec 2021 23:18:14: #1 total tags in treatment: 11893725 INFO @ Wed, 08 Dec 2021 23:18:14: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:18:14: #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 23:18:14: #1 tags after filtering in treatment: 8227567 INFO @ Wed, 08 Dec 2021 23:18:14: #1 Redundant rate of treatment: 0.31 INFO @ Wed, 08 Dec 2021 23:18:14: #1 finished! INFO @ Wed, 08 Dec 2021 23:18:14: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:18:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:18:14: #1 tag size is determined as 125 bps INFO @ Wed, 08 Dec 2021 23:18:14: #1 tag size = 125 INFO @ Wed, 08 Dec 2021 23:18:14: #1 total tags in treatment: 11893725 INFO @ Wed, 08 Dec 2021 23:18:14: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:18:14: #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 23:18:14: #2 number of paired peaks: 964 WARNING @ Wed, 08 Dec 2021 23:18:14: Fewer paired peaks (964) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 964 pairs to build model! INFO @ Wed, 08 Dec 2021 23:18:14: start model_add_line... INFO @ Wed, 08 Dec 2021 23:18:14: start X-correlation... INFO @ Wed, 08 Dec 2021 23:18:14: end of X-cor INFO @ Wed, 08 Dec 2021 23:18:14: #2 finished! INFO @ Wed, 08 Dec 2021 23:18:14: #2 predicted fragment length is 232 bps INFO @ Wed, 08 Dec 2021 23:18:14: #2 alternative fragment length(s) may be 232 bps INFO @ Wed, 08 Dec 2021 23:18:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845643/SRX8845643.05_model.r INFO @ Wed, 08 Dec 2021 23:18:15: #1 tags after filtering in treatment: 8227567 INFO @ Wed, 08 Dec 2021 23:18:15: #1 Redundant rate of treatment: 0.31 INFO @ Wed, 08 Dec 2021 23:18:15: #1 finished! INFO @ Wed, 08 Dec 2021 23:18:15: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:18:15: #2 looking for paired plus/minus strand peaks... WARNING @ Wed, 08 Dec 2021 23:18:15: #2 Since the d (232) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:18:15: #2 You may need to consider one of the other alternative d(s): 232 WARNING @ Wed, 08 Dec 2021 23:18:15: #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 23:18:15: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:18:15: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:18:15: #2 number of paired peaks: 964 WARNING @ Wed, 08 Dec 2021 23:18:15: Fewer paired peaks (964) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 964 pairs to build model! INFO @ Wed, 08 Dec 2021 23:18:15: start model_add_line... INFO @ Wed, 08 Dec 2021 23:18:15: start X-correlation... INFO @ Wed, 08 Dec 2021 23:18:15: end of X-cor INFO @ Wed, 08 Dec 2021 23:18:15: #2 finished! INFO @ Wed, 08 Dec 2021 23:18:15: #2 predicted fragment length is 232 bps INFO @ Wed, 08 Dec 2021 23:18:15: #2 alternative fragment length(s) may be 232 bps INFO @ Wed, 08 Dec 2021 23:18:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845643/SRX8845643.10_model.r WARNING @ Wed, 08 Dec 2021 23:18:15: #2 Since the d (232) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:18:15: #2 You may need to consider one of the other alternative d(s): 232 WARNING @ Wed, 08 Dec 2021 23:18:15: #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 23:18:15: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:18:15: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:18:16: 20000000 INFO @ Wed, 08 Dec 2021 23:18:23: 21000000 INFO @ Wed, 08 Dec 2021 23:18:30: 22000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 23:18:33: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:18:34: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:18:37: 23000000 INFO @ Wed, 08 Dec 2021 23:18:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845643/SRX8845643.10_peaks.xls INFO @ Wed, 08 Dec 2021 23:18:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845643/SRX8845643.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:18:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845643/SRX8845643.10_summits.bed INFO @ Wed, 08 Dec 2021 23:18:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4230 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:18:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845643/SRX8845643.05_peaks.xls INFO @ Wed, 08 Dec 2021 23:18:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845643/SRX8845643.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:18:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845643/SRX8845643.05_summits.bed INFO @ Wed, 08 Dec 2021 23:18:43: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6973 records, 4 fields): 45 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:18:44: 24000000 INFO @ Wed, 08 Dec 2021 23:18:51: 25000000 INFO @ Wed, 08 Dec 2021 23:18:58: 26000000 INFO @ Wed, 08 Dec 2021 23:19:04: 27000000 INFO @ Wed, 08 Dec 2021 23:19:11: 28000000 INFO @ Wed, 08 Dec 2021 23:19:14: #1 tag size is determined as 125 bps INFO @ Wed, 08 Dec 2021 23:19:14: #1 tag size = 125 INFO @ Wed, 08 Dec 2021 23:19:14: #1 total tags in treatment: 11893725 INFO @ Wed, 08 Dec 2021 23:19:14: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:19:14: #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 23:19:15: #1 tags after filtering in treatment: 8227567 INFO @ Wed, 08 Dec 2021 23:19:15: #1 Redundant rate of treatment: 0.31 INFO @ Wed, 08 Dec 2021 23:19:15: #1 finished! INFO @ Wed, 08 Dec 2021 23:19:15: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:19:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:19:15: #2 number of paired peaks: 964 WARNING @ Wed, 08 Dec 2021 23:19:15: Fewer paired peaks (964) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 964 pairs to build model! INFO @ Wed, 08 Dec 2021 23:19:15: start model_add_line... INFO @ Wed, 08 Dec 2021 23:19:15: start X-correlation... INFO @ Wed, 08 Dec 2021 23:19:15: end of X-cor INFO @ Wed, 08 Dec 2021 23:19:15: #2 finished! INFO @ Wed, 08 Dec 2021 23:19:15: #2 predicted fragment length is 232 bps INFO @ Wed, 08 Dec 2021 23:19:15: #2 alternative fragment length(s) may be 232 bps INFO @ Wed, 08 Dec 2021 23:19:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845643/SRX8845643.20_model.r WARNING @ Wed, 08 Dec 2021 23:19:15: #2 Since the d (232) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:19:15: #2 You may need to consider one of the other alternative d(s): 232 WARNING @ Wed, 08 Dec 2021 23:19:15: #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 23:19:15: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:19:15: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:19:35: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:19:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845643/SRX8845643.20_peaks.xls INFO @ Wed, 08 Dec 2021 23:19:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845643/SRX8845643.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:19:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845643/SRX8845643.20_summits.bed INFO @ Wed, 08 Dec 2021 23:19:43: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1893 records, 4 fields): 3 millis CompletedMACS2peakCalling