Job ID = 14159553 SRX = SRX8845647 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 32587283 spots for SRR12345954/SRR12345954.sra Written 32587283 spots for SRR12345954/SRR12345954.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160029 ("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: 00:41:55 32587283 reads; of these: 32587283 (100.00%) were paired; of these: 21072963 (64.67%) aligned concordantly 0 times 9995208 (30.67%) aligned concordantly exactly 1 time 1519112 (4.66%) aligned concordantly >1 times ---- 21072963 pairs aligned concordantly 0 times; of these: 1721323 (8.17%) aligned discordantly 1 time ---- 19351640 pairs aligned 0 times concordantly or discordantly; of these: 38703280 mates make up the pairs; of these: 37572655 (97.08%) aligned 0 times 299711 (0.77%) aligned exactly 1 time 830914 (2.15%) aligned >1 times 42.35% overall alignment rate Time searching: 00:41:55 Overall time: 00:41:55 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 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] 4561479 / 13181983 = 0.3460 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 23:26:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845647/SRX8845647.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845647/SRX8845647.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845647/SRX8845647.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845647/SRX8845647.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 23:26:14: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:26:14: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:26:30: 1000000 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 23:26:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845647/SRX8845647.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845647/SRX8845647.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845647/SRX8845647.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845647/SRX8845647.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 23:26:44: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:26:44: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:26:46: 2000000 INFO @ Wed, 08 Dec 2021 23:26:57: 1000000 INFO @ Wed, 08 Dec 2021 23:27:02: 3000000 INFO @ Wed, 08 Dec 2021 23:27:10: 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 23:27:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845647/SRX8845647.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845647/SRX8845647.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845647/SRX8845647.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845647/SRX8845647.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 23:27:14: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:27:14: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:27:18: 4000000 INFO @ Wed, 08 Dec 2021 23:27:23: 3000000 INFO @ Wed, 08 Dec 2021 23:27:26: 1000000 INFO @ Wed, 08 Dec 2021 23:27:35: 5000000 INFO @ Wed, 08 Dec 2021 23:27:36: 4000000 INFO @ Wed, 08 Dec 2021 23:27:37: 2000000 INFO @ Wed, 08 Dec 2021 23:27:49: 3000000 INFO @ Wed, 08 Dec 2021 23:27:49: 5000000 INFO @ Wed, 08 Dec 2021 23:27:51: 6000000 INFO @ Wed, 08 Dec 2021 23:28:00: 4000000 INFO @ Wed, 08 Dec 2021 23:28:02: 6000000 INFO @ Wed, 08 Dec 2021 23:28:07: 7000000 INFO @ Wed, 08 Dec 2021 23:28:12: 5000000 INFO @ Wed, 08 Dec 2021 23:28:15: 7000000 INFO @ Wed, 08 Dec 2021 23:28:23: 6000000 INFO @ Wed, 08 Dec 2021 23:28:23: 8000000 INFO @ Wed, 08 Dec 2021 23:28:27: 8000000 INFO @ Wed, 08 Dec 2021 23:28:35: 7000000 INFO @ Wed, 08 Dec 2021 23:28:39: 9000000 INFO @ Wed, 08 Dec 2021 23:28:40: 9000000 INFO @ Wed, 08 Dec 2021 23:28:47: 8000000 INFO @ Wed, 08 Dec 2021 23:28:50: 10000000 INFO @ Wed, 08 Dec 2021 23:28:58: 10000000 INFO @ Wed, 08 Dec 2021 23:28:58: 9000000 INFO @ Wed, 08 Dec 2021 23:29:02: 11000000 INFO @ Wed, 08 Dec 2021 23:29:10: 10000000 INFO @ Wed, 08 Dec 2021 23:29:14: 12000000 INFO @ Wed, 08 Dec 2021 23:29:15: 11000000 INFO @ Wed, 08 Dec 2021 23:29:22: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 23:29:26: 13000000 INFO @ Wed, 08 Dec 2021 23:29:32: 12000000 INFO @ Wed, 08 Dec 2021 23:29:35: 12000000 INFO @ Wed, 08 Dec 2021 23:29:38: 14000000 INFO @ Wed, 08 Dec 2021 23:29:47: 13000000 INFO @ Wed, 08 Dec 2021 23:29:50: 13000000 INFO @ Wed, 08 Dec 2021 23:29:50: 15000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 23:29:59: 14000000 INFO @ Wed, 08 Dec 2021 23:30:03: 16000000 INFO @ Wed, 08 Dec 2021 23:30:06: 14000000 INFO @ Wed, 08 Dec 2021 23:30:12: 15000000 INFO @ Wed, 08 Dec 2021 23:30:15: 17000000 INFO @ Wed, 08 Dec 2021 23:30:21: 15000000 INFO @ Wed, 08 Dec 2021 23:30:24: 16000000 INFO @ Wed, 08 Dec 2021 23:30:27: 18000000 INFO @ Wed, 08 Dec 2021 23:30:32: #1 tag size is determined as 125 bps INFO @ Wed, 08 Dec 2021 23:30:32: #1 tag size = 125 INFO @ Wed, 08 Dec 2021 23:30:32: #1 total tags in treatment: 7555238 INFO @ Wed, 08 Dec 2021 23:30:32: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:30:32: #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 23:30:32: #1 tags after filtering in treatment: 5624932 INFO @ Wed, 08 Dec 2021 23:30:32: #1 Redundant rate of treatment: 0.26 INFO @ Wed, 08 Dec 2021 23:30:32: #1 finished! INFO @ Wed, 08 Dec 2021 23:30:32: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:30:32: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:30:33: #2 number of paired peaks: 1326 INFO @ Wed, 08 Dec 2021 23:30:33: start model_add_line... INFO @ Wed, 08 Dec 2021 23:30:33: start X-correlation... INFO @ Wed, 08 Dec 2021 23:30:33: end of X-cor INFO @ Wed, 08 Dec 2021 23:30:33: #2 finished! INFO @ Wed, 08 Dec 2021 23:30:33: #2 predicted fragment length is 226 bps INFO @ Wed, 08 Dec 2021 23:30:33: #2 alternative fragment length(s) may be 226 bps INFO @ Wed, 08 Dec 2021 23:30:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845647/SRX8845647.10_model.r WARNING @ Wed, 08 Dec 2021 23:30:33: #2 Since the d (226) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:30:33: #2 You may need to consider one of the other alternative d(s): 226 WARNING @ Wed, 08 Dec 2021 23:30:33: #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 23:30:33: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:30:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:30:35: 17000000 INFO @ Wed, 08 Dec 2021 23:30:37: 16000000 INFO @ Wed, 08 Dec 2021 23:30:46: 18000000 INFO @ Wed, 08 Dec 2021 23:30:52: #1 tag size is determined as 125 bps INFO @ Wed, 08 Dec 2021 23:30:52: #1 tag size = 125 INFO @ Wed, 08 Dec 2021 23:30:52: #1 total tags in treatment: 7555238 INFO @ Wed, 08 Dec 2021 23:30:52: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:30:52: #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 23:30:52: #1 tags after filtering in treatment: 5624932 INFO @ Wed, 08 Dec 2021 23:30:52: #1 Redundant rate of treatment: 0.26 INFO @ Wed, 08 Dec 2021 23:30:52: #1 finished! INFO @ Wed, 08 Dec 2021 23:30:52: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:30:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:30:52: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:30:52: #2 number of paired peaks: 1326 INFO @ Wed, 08 Dec 2021 23:30:52: start model_add_line... INFO @ Wed, 08 Dec 2021 23:30:52: start X-correlation... INFO @ Wed, 08 Dec 2021 23:30:52: end of X-cor INFO @ Wed, 08 Dec 2021 23:30:52: #2 finished! INFO @ Wed, 08 Dec 2021 23:30:52: #2 predicted fragment length is 226 bps INFO @ Wed, 08 Dec 2021 23:30:52: #2 alternative fragment length(s) may be 226 bps INFO @ Wed, 08 Dec 2021 23:30:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845647/SRX8845647.20_model.r WARNING @ Wed, 08 Dec 2021 23:30:52: #2 Since the d (226) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:30:52: #2 You may need to consider one of the other alternative d(s): 226 WARNING @ Wed, 08 Dec 2021 23:30:52: #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 23:30:52: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:30:52: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:30:53: 17000000 INFO @ Wed, 08 Dec 2021 23:31:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845647/SRX8845647.10_peaks.xls INFO @ Wed, 08 Dec 2021 23:31:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845647/SRX8845647.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:31:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845647/SRX8845647.10_summits.bed INFO @ Wed, 08 Dec 2021 23:31:01: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3741 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:31:11: 18000000 INFO @ Wed, 08 Dec 2021 23:31:11: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:31:18: #1 tag size is determined as 125 bps INFO @ Wed, 08 Dec 2021 23:31:18: #1 tag size = 125 INFO @ Wed, 08 Dec 2021 23:31:18: #1 total tags in treatment: 7555238 INFO @ Wed, 08 Dec 2021 23:31:18: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:31:18: #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 23:31:19: #1 tags after filtering in treatment: 5624932 INFO @ Wed, 08 Dec 2021 23:31:19: #1 Redundant rate of treatment: 0.26 INFO @ Wed, 08 Dec 2021 23:31:19: #1 finished! INFO @ Wed, 08 Dec 2021 23:31:19: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:31:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:31:19: #2 number of paired peaks: 1326 INFO @ Wed, 08 Dec 2021 23:31:19: start model_add_line... INFO @ Wed, 08 Dec 2021 23:31:19: start X-correlation... INFO @ Wed, 08 Dec 2021 23:31:19: end of X-cor INFO @ Wed, 08 Dec 2021 23:31:19: #2 finished! INFO @ Wed, 08 Dec 2021 23:31:19: #2 predicted fragment length is 226 bps INFO @ Wed, 08 Dec 2021 23:31:19: #2 alternative fragment length(s) may be 226 bps INFO @ Wed, 08 Dec 2021 23:31:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845647/SRX8845647.05_model.r WARNING @ Wed, 08 Dec 2021 23:31:19: #2 Since the d (226) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 23:31:19: #2 You may need to consider one of the other alternative d(s): 226 WARNING @ Wed, 08 Dec 2021 23:31:19: #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 23:31:19: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:31:19: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:31:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845647/SRX8845647.20_peaks.xls INFO @ Wed, 08 Dec 2021 23:31:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845647/SRX8845647.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:31:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845647/SRX8845647.20_summits.bed INFO @ Wed, 08 Dec 2021 23:31:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1592 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 23:31:40: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 23:31:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845647/SRX8845647.05_peaks.xls INFO @ Wed, 08 Dec 2021 23:31:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845647/SRX8845647.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 23:31:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845647/SRX8845647.05_summits.bed INFO @ Wed, 08 Dec 2021 23:31:50: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (6336 records, 4 fields): 10 millis CompletedMACS2peakCalling