Job ID = 12264767 SRX = SRX3029132 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 24717131 spots for SRR5860432/SRR5860432.sra Written 24717131 spots for SRR5860432/SRR5860432.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265378 ("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: 00:27:01 24717131 reads; of these: 24717131 (100.00%) were paired; of these: 7692904 (31.12%) aligned concordantly 0 times 14972260 (60.57%) aligned concordantly exactly 1 time 2051967 (8.30%) aligned concordantly >1 times ---- 7692904 pairs aligned concordantly 0 times; of these: 2163504 (28.12%) aligned discordantly 1 time ---- 5529400 pairs aligned 0 times concordantly or discordantly; of these: 11058800 mates make up the pairs; of these: 9931173 (89.80%) aligned 0 times 512286 (4.63%) aligned exactly 1 time 615341 (5.56%) aligned >1 times 79.91% overall alignment rate Time searching: 00:27:01 Overall time: 00:27:01 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 20 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] 5270946 / 19007168 = 0.2773 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:41:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3029132/SRX3029132.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3029132/SRX3029132.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3029132/SRX3029132.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3029132/SRX3029132.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 @ Sat, 03 Apr 2021 06:41:13: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:41:13: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:41:20: 1000000 INFO @ Sat, 03 Apr 2021 06:41:26: 2000000 INFO @ Sat, 03 Apr 2021 06:41:32: 3000000 INFO @ Sat, 03 Apr 2021 06:41:39: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:41:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3029132/SRX3029132.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3029132/SRX3029132.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3029132/SRX3029132.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3029132/SRX3029132.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 @ Sat, 03 Apr 2021 06:41:43: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:41:43: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:41:45: 5000000 INFO @ Sat, 03 Apr 2021 06:41:50: 1000000 INFO @ Sat, 03 Apr 2021 06:41:52: 6000000 INFO @ Sat, 03 Apr 2021 06:41:56: 2000000 INFO @ Sat, 03 Apr 2021 06:41:58: 7000000 INFO @ Sat, 03 Apr 2021 06:42:02: 3000000 INFO @ Sat, 03 Apr 2021 06:42:05: 8000000 INFO @ Sat, 03 Apr 2021 06:42:09: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:42:12: 9000000 INFO @ Sat, 03 Apr 2021 06:42:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3029132/SRX3029132.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3029132/SRX3029132.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3029132/SRX3029132.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3029132/SRX3029132.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 @ Sat, 03 Apr 2021 06:42:13: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:42:13: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:42:15: 5000000 INFO @ Sat, 03 Apr 2021 06:42:18: 10000000 INFO @ Sat, 03 Apr 2021 06:42:20: 1000000 INFO @ Sat, 03 Apr 2021 06:42:22: 6000000 INFO @ Sat, 03 Apr 2021 06:42:25: 11000000 INFO @ Sat, 03 Apr 2021 06:42:28: 2000000 INFO @ Sat, 03 Apr 2021 06:42:30: 7000000 INFO @ Sat, 03 Apr 2021 06:42:32: 12000000 INFO @ Sat, 03 Apr 2021 06:42:35: 3000000 INFO @ Sat, 03 Apr 2021 06:42:37: 8000000 INFO @ Sat, 03 Apr 2021 06:42:39: 13000000 INFO @ Sat, 03 Apr 2021 06:42:42: 4000000 INFO @ Sat, 03 Apr 2021 06:42:44: 9000000 INFO @ Sat, 03 Apr 2021 06:42:45: 14000000 INFO @ Sat, 03 Apr 2021 06:42:49: 5000000 INFO @ Sat, 03 Apr 2021 06:42:51: 10000000 INFO @ Sat, 03 Apr 2021 06:42:52: 15000000 INFO @ Sat, 03 Apr 2021 06:42:57: 6000000 INFO @ Sat, 03 Apr 2021 06:42:59: 11000000 INFO @ Sat, 03 Apr 2021 06:42:59: 16000000 INFO @ Sat, 03 Apr 2021 06:43:04: 7000000 INFO @ Sat, 03 Apr 2021 06:43:06: 17000000 INFO @ Sat, 03 Apr 2021 06:43:06: 12000000 INFO @ Sat, 03 Apr 2021 06:43:11: 8000000 INFO @ Sat, 03 Apr 2021 06:43:13: 18000000 INFO @ Sat, 03 Apr 2021 06:43:13: 13000000 INFO @ Sat, 03 Apr 2021 06:43:18: 9000000 INFO @ Sat, 03 Apr 2021 06:43:19: 19000000 INFO @ Sat, 03 Apr 2021 06:43:20: 14000000 INFO @ Sat, 03 Apr 2021 06:43:25: 10000000 INFO @ Sat, 03 Apr 2021 06:43:26: 20000000 INFO @ Sat, 03 Apr 2021 06:43:27: 15000000 INFO @ Sat, 03 Apr 2021 06:43:33: 11000000 INFO @ Sat, 03 Apr 2021 06:43:33: 21000000 INFO @ Sat, 03 Apr 2021 06:43:35: 16000000 INFO @ Sat, 03 Apr 2021 06:43:40: 22000000 INFO @ Sat, 03 Apr 2021 06:43:40: 12000000 INFO @ Sat, 03 Apr 2021 06:43:42: 17000000 INFO @ Sat, 03 Apr 2021 06:43:47: 23000000 INFO @ Sat, 03 Apr 2021 06:43:48: 13000000 INFO @ Sat, 03 Apr 2021 06:43:50: 18000000 INFO @ Sat, 03 Apr 2021 06:43:54: 24000000 INFO @ Sat, 03 Apr 2021 06:43:55: 14000000 INFO @ Sat, 03 Apr 2021 06:43:57: 19000000 INFO @ Sat, 03 Apr 2021 06:44:01: 25000000 INFO @ Sat, 03 Apr 2021 06:44:02: 15000000 INFO @ Sat, 03 Apr 2021 06:44:04: 20000000 INFO @ Sat, 03 Apr 2021 06:44:07: 26000000 INFO @ Sat, 03 Apr 2021 06:44:09: 16000000 INFO @ Sat, 03 Apr 2021 06:44:11: 21000000 INFO @ Sat, 03 Apr 2021 06:44:14: 27000000 INFO @ Sat, 03 Apr 2021 06:44:16: 17000000 INFO @ Sat, 03 Apr 2021 06:44:18: 22000000 INFO @ Sat, 03 Apr 2021 06:44:20: 28000000 INFO @ Sat, 03 Apr 2021 06:44:23: 18000000 INFO @ Sat, 03 Apr 2021 06:44:25: 23000000 INFO @ Sat, 03 Apr 2021 06:44:27: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 06:44:27: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 06:44:27: #1 total tags in treatment: 12280621 INFO @ Sat, 03 Apr 2021 06:44:27: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:44:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:44:27: #1 tags after filtering in treatment: 9145517 INFO @ Sat, 03 Apr 2021 06:44:27: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 03 Apr 2021 06:44:27: #1 finished! INFO @ Sat, 03 Apr 2021 06:44:27: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:44:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:44:27: #2 number of paired peaks: 530 WARNING @ Sat, 03 Apr 2021 06:44:27: Fewer paired peaks (530) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 530 pairs to build model! INFO @ Sat, 03 Apr 2021 06:44:27: start model_add_line... INFO @ Sat, 03 Apr 2021 06:44:28: start X-correlation... INFO @ Sat, 03 Apr 2021 06:44:28: end of X-cor INFO @ Sat, 03 Apr 2021 06:44:28: #2 finished! INFO @ Sat, 03 Apr 2021 06:44:28: #2 predicted fragment length is 117 bps INFO @ Sat, 03 Apr 2021 06:44:28: #2 alternative fragment length(s) may be 117 bps INFO @ Sat, 03 Apr 2021 06:44:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3029132/SRX3029132.05_model.r WARNING @ Sat, 03 Apr 2021 06:44:28: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:44:28: #2 You may need to consider one of the other alternative d(s): 117 WARNING @ Sat, 03 Apr 2021 06:44:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:44:28: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:44:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:44:30: 19000000 INFO @ Sat, 03 Apr 2021 06:44:32: 24000000 INFO @ Sat, 03 Apr 2021 06:44:37: 20000000 INFO @ Sat, 03 Apr 2021 06:44:39: 25000000 INFO @ Sat, 03 Apr 2021 06:44:44: 21000000 INFO @ Sat, 03 Apr 2021 06:44:46: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:44:46: 26000000 INFO @ Sat, 03 Apr 2021 06:44:50: 22000000 INFO @ Sat, 03 Apr 2021 06:44:53: 27000000 INFO @ Sat, 03 Apr 2021 06:44:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3029132/SRX3029132.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:44:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3029132/SRX3029132.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:44:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3029132/SRX3029132.05_summits.bed INFO @ Sat, 03 Apr 2021 06:44:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6222 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:44:57: 23000000 INFO @ Sat, 03 Apr 2021 06:44:59: 28000000 INFO @ Sat, 03 Apr 2021 06:45:04: 24000000 INFO @ Sat, 03 Apr 2021 06:45:05: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 06:45:05: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 06:45:05: #1 total tags in treatment: 12280621 INFO @ Sat, 03 Apr 2021 06:45:05: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:45:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:45:06: #1 tags after filtering in treatment: 9145517 INFO @ Sat, 03 Apr 2021 06:45:06: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 03 Apr 2021 06:45:06: #1 finished! INFO @ Sat, 03 Apr 2021 06:45:06: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:45:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:45:06: #2 number of paired peaks: 530 WARNING @ Sat, 03 Apr 2021 06:45:06: Fewer paired peaks (530) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 530 pairs to build model! INFO @ Sat, 03 Apr 2021 06:45:06: start model_add_line... INFO @ Sat, 03 Apr 2021 06:45:06: start X-correlation... INFO @ Sat, 03 Apr 2021 06:45:07: end of X-cor INFO @ Sat, 03 Apr 2021 06:45:07: #2 finished! INFO @ Sat, 03 Apr 2021 06:45:07: #2 predicted fragment length is 117 bps INFO @ Sat, 03 Apr 2021 06:45:07: #2 alternative fragment length(s) may be 117 bps INFO @ Sat, 03 Apr 2021 06:45:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3029132/SRX3029132.10_model.r WARNING @ Sat, 03 Apr 2021 06:45:07: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:45:07: #2 You may need to consider one of the other alternative d(s): 117 WARNING @ Sat, 03 Apr 2021 06:45:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:45:07: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:45:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:45:10: 25000000 INFO @ Sat, 03 Apr 2021 06:45:17: 26000000 INFO @ Sat, 03 Apr 2021 06:45:23: 27000000 INFO @ Sat, 03 Apr 2021 06:45:25: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:45:29: 28000000 INFO @ Sat, 03 Apr 2021 06:45:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3029132/SRX3029132.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:45:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3029132/SRX3029132.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:45:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3029132/SRX3029132.10_summits.bed INFO @ Sat, 03 Apr 2021 06:45:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3437 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:45:35: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 06:45:35: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 06:45:35: #1 total tags in treatment: 12280621 INFO @ Sat, 03 Apr 2021 06:45:35: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:45:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:45:35: #1 tags after filtering in treatment: 9145517 INFO @ Sat, 03 Apr 2021 06:45:35: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 03 Apr 2021 06:45:35: #1 finished! INFO @ Sat, 03 Apr 2021 06:45:35: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:45:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:45:36: #2 number of paired peaks: 530 WARNING @ Sat, 03 Apr 2021 06:45:36: Fewer paired peaks (530) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 530 pairs to build model! INFO @ Sat, 03 Apr 2021 06:45:36: start model_add_line... INFO @ Sat, 03 Apr 2021 06:45:36: start X-correlation... INFO @ Sat, 03 Apr 2021 06:45:36: end of X-cor INFO @ Sat, 03 Apr 2021 06:45:36: #2 finished! INFO @ Sat, 03 Apr 2021 06:45:36: #2 predicted fragment length is 117 bps INFO @ Sat, 03 Apr 2021 06:45:36: #2 alternative fragment length(s) may be 117 bps INFO @ Sat, 03 Apr 2021 06:45:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3029132/SRX3029132.20_model.r WARNING @ Sat, 03 Apr 2021 06:45:36: #2 Since the d (117) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:45:36: #2 You may need to consider one of the other alternative d(s): 117 WARNING @ Sat, 03 Apr 2021 06:45:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:45:36: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:45:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:45:54: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:46:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3029132/SRX3029132.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:46:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3029132/SRX3029132.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:46:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3029132/SRX3029132.20_summits.bed INFO @ Sat, 03 Apr 2021 06:46:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1476 records, 4 fields): 9 millis CompletedMACS2peakCalling