Job ID = 12264757 SRX = SRX3029122 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 28757519 spots for SRR5860422/SRR5860422.sra Written 28757519 spots for SRR5860422/SRR5860422.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265399 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:31:25 28757519 reads; of these: 28757519 (100.00%) were paired; of these: 10075345 (35.04%) aligned concordantly 0 times 16013874 (55.69%) aligned concordantly exactly 1 time 2668300 (9.28%) aligned concordantly >1 times ---- 10075345 pairs aligned concordantly 0 times; of these: 3229402 (32.05%) aligned discordantly 1 time ---- 6845943 pairs aligned 0 times concordantly or discordantly; of these: 13691886 mates make up the pairs; of these: 12079382 (88.22%) aligned 0 times 700891 (5.12%) aligned exactly 1 time 911613 (6.66%) aligned >1 times 79.00% overall alignment rate Time searching: 00:31:26 Overall time: 00:31:26 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] 4550934 / 21669121 = 0.2100 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 06:46:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3029122/SRX3029122.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3029122/SRX3029122.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3029122/SRX3029122.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3029122/SRX3029122.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 06:46:47: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:46:47: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:46:52: 1000000 INFO @ Sat, 03 Apr 2021 06:46:58: 2000000 INFO @ Sat, 03 Apr 2021 06:47:03: 3000000 INFO @ Sat, 03 Apr 2021 06:47:08: 4000000 INFO @ Sat, 03 Apr 2021 06:47:13: 5000000 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 06:47:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3029122/SRX3029122.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3029122/SRX3029122.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3029122/SRX3029122.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3029122/SRX3029122.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 06:47:17: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:47:17: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:47:19: 6000000 INFO @ Sat, 03 Apr 2021 06:47:23: 1000000 INFO @ Sat, 03 Apr 2021 06:47:24: 7000000 INFO @ Sat, 03 Apr 2021 06:47:28: 2000000 INFO @ Sat, 03 Apr 2021 06:47:29: 8000000 INFO @ Sat, 03 Apr 2021 06:47:33: 3000000 INFO @ Sat, 03 Apr 2021 06:47:34: 9000000 INFO @ Sat, 03 Apr 2021 06:47:38: 4000000 INFO @ Sat, 03 Apr 2021 06:47:40: 10000000 INFO @ Sat, 03 Apr 2021 06:47:45: 5000000 INFO @ Sat, 03 Apr 2021 06:47:45: 11000000 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 06:47:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3029122/SRX3029122.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3029122/SRX3029122.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3029122/SRX3029122.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3029122/SRX3029122.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 06:47:47: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:47:47: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:47:50: 6000000 INFO @ Sat, 03 Apr 2021 06:47:51: 12000000 INFO @ Sat, 03 Apr 2021 06:47:53: 1000000 INFO @ Sat, 03 Apr 2021 06:47:56: 7000000 INFO @ Sat, 03 Apr 2021 06:47:56: 13000000 INFO @ Sat, 03 Apr 2021 06:47:59: 2000000 INFO @ Sat, 03 Apr 2021 06:48:02: 8000000 INFO @ Sat, 03 Apr 2021 06:48:02: 14000000 INFO @ Sat, 03 Apr 2021 06:48:05: 3000000 INFO @ Sat, 03 Apr 2021 06:48:07: 15000000 INFO @ Sat, 03 Apr 2021 06:48:07: 9000000 INFO @ Sat, 03 Apr 2021 06:48:11: 4000000 INFO @ Sat, 03 Apr 2021 06:48:12: 16000000 INFO @ Sat, 03 Apr 2021 06:48:14: 10000000 INFO @ Sat, 03 Apr 2021 06:48:17: 5000000 INFO @ Sat, 03 Apr 2021 06:48:17: 17000000 INFO @ Sat, 03 Apr 2021 06:48:20: 11000000 INFO @ Sat, 03 Apr 2021 06:48:23: 6000000 INFO @ Sat, 03 Apr 2021 06:48:23: 18000000 INFO @ Sat, 03 Apr 2021 06:48:25: 12000000 INFO @ Sat, 03 Apr 2021 06:48:28: 19000000 INFO @ Sat, 03 Apr 2021 06:48:28: 7000000 INFO @ Sat, 03 Apr 2021 06:48:31: 13000000 INFO @ Sat, 03 Apr 2021 06:48:33: 20000000 INFO @ Sat, 03 Apr 2021 06:48:34: 8000000 INFO @ Sat, 03 Apr 2021 06:48:37: 14000000 INFO @ Sat, 03 Apr 2021 06:48:38: 21000000 INFO @ Sat, 03 Apr 2021 06:48:40: 9000000 INFO @ Sat, 03 Apr 2021 06:48:43: 15000000 INFO @ Sat, 03 Apr 2021 06:48:44: 22000000 INFO @ Sat, 03 Apr 2021 06:48:46: 10000000 INFO @ Sat, 03 Apr 2021 06:48:49: 16000000 INFO @ Sat, 03 Apr 2021 06:48:49: 23000000 INFO @ Sat, 03 Apr 2021 06:48:52: 11000000 INFO @ Sat, 03 Apr 2021 06:48:54: 24000000 INFO @ Sat, 03 Apr 2021 06:48:55: 17000000 INFO @ Sat, 03 Apr 2021 06:48:58: 12000000 INFO @ Sat, 03 Apr 2021 06:49:00: 25000000 INFO @ Sat, 03 Apr 2021 06:49:01: 18000000 INFO @ Sat, 03 Apr 2021 06:49:04: 13000000 INFO @ Sat, 03 Apr 2021 06:49:05: 26000000 INFO @ Sat, 03 Apr 2021 06:49:06: 19000000 INFO @ Sat, 03 Apr 2021 06:49:10: 14000000 INFO @ Sat, 03 Apr 2021 06:49:10: 27000000 INFO @ Sat, 03 Apr 2021 06:49:12: 20000000 INFO @ Sat, 03 Apr 2021 06:49:16: 28000000 INFO @ Sat, 03 Apr 2021 06:49:16: 15000000 INFO @ Sat, 03 Apr 2021 06:49:19: 21000000 INFO @ Sat, 03 Apr 2021 06:49:21: 29000000 INFO @ Sat, 03 Apr 2021 06:49:22: 16000000 INFO @ Sat, 03 Apr 2021 06:49:25: 22000000 INFO @ Sat, 03 Apr 2021 06:49:27: 30000000 INFO @ Sat, 03 Apr 2021 06:49:28: 17000000 INFO @ Sat, 03 Apr 2021 06:49:30: 23000000 INFO @ Sat, 03 Apr 2021 06:49:32: 31000000 INFO @ Sat, 03 Apr 2021 06:49:34: 18000000 INFO @ Sat, 03 Apr 2021 06:49:36: 24000000 INFO @ Sat, 03 Apr 2021 06:49:38: 32000000 INFO @ Sat, 03 Apr 2021 06:49:40: 19000000 INFO @ Sat, 03 Apr 2021 06:49:42: 25000000 INFO @ Sat, 03 Apr 2021 06:49:43: 33000000 INFO @ Sat, 03 Apr 2021 06:49:45: 20000000 INFO @ Sat, 03 Apr 2021 06:49:48: 26000000 INFO @ Sat, 03 Apr 2021 06:49:49: 34000000 INFO @ Sat, 03 Apr 2021 06:49:52: 21000000 INFO @ Sat, 03 Apr 2021 06:49:54: 35000000 INFO @ Sat, 03 Apr 2021 06:49:54: 27000000 INFO @ Sat, 03 Apr 2021 06:49:58: 22000000 INFO @ Sat, 03 Apr 2021 06:49:59: 36000000 INFO @ Sat, 03 Apr 2021 06:50:00: 28000000 INFO @ Sat, 03 Apr 2021 06:50:01: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 06:50:01: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 06:50:01: #1 total tags in treatment: 14955747 INFO @ Sat, 03 Apr 2021 06:50:01: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:50:01: #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 06:50:01: #1 tags after filtering in treatment: 9952410 INFO @ Sat, 03 Apr 2021 06:50:01: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 03 Apr 2021 06:50:01: #1 finished! INFO @ Sat, 03 Apr 2021 06:50:01: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:50:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:50:02: #2 number of paired peaks: 805 WARNING @ Sat, 03 Apr 2021 06:50:02: Fewer paired peaks (805) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 805 pairs to build model! INFO @ Sat, 03 Apr 2021 06:50:02: start model_add_line... INFO @ Sat, 03 Apr 2021 06:50:02: start X-correlation... INFO @ Sat, 03 Apr 2021 06:50:02: end of X-cor INFO @ Sat, 03 Apr 2021 06:50:02: #2 finished! INFO @ Sat, 03 Apr 2021 06:50:02: #2 predicted fragment length is 113 bps INFO @ Sat, 03 Apr 2021 06:50:02: #2 alternative fragment length(s) may be 113 bps INFO @ Sat, 03 Apr 2021 06:50:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3029122/SRX3029122.05_model.r WARNING @ Sat, 03 Apr 2021 06:50:02: #2 Since the d (113) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:50:02: #2 You may need to consider one of the other alternative d(s): 113 WARNING @ Sat, 03 Apr 2021 06:50:02: #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 06:50:02: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:50:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:50:04: 23000000 INFO @ Sat, 03 Apr 2021 06:50:05: 29000000 INFO @ Sat, 03 Apr 2021 06:50:09: 24000000 INFO @ Sat, 03 Apr 2021 06:50:11: 30000000 INFO @ Sat, 03 Apr 2021 06:50:15: 25000000 INFO @ Sat, 03 Apr 2021 06:50:17: 31000000 INFO @ Sat, 03 Apr 2021 06:50:21: 26000000 INFO @ Sat, 03 Apr 2021 06:50:22: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:50:23: 32000000 INFO @ Sat, 03 Apr 2021 06:50:27: 27000000 INFO @ Sat, 03 Apr 2021 06:50:29: 33000000 INFO @ Sat, 03 Apr 2021 06:50:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3029122/SRX3029122.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:50:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3029122/SRX3029122.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:50:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3029122/SRX3029122.05_summits.bed INFO @ Sat, 03 Apr 2021 06:50:32: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (10252 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:50:33: 28000000 INFO @ Sat, 03 Apr 2021 06:50:34: 34000000 INFO @ Sat, 03 Apr 2021 06:50:39: 29000000 INFO @ Sat, 03 Apr 2021 06:50:40: 35000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:50:45: 30000000 INFO @ Sat, 03 Apr 2021 06:50:46: 36000000 INFO @ Sat, 03 Apr 2021 06:50:48: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 06:50:48: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 06:50:48: #1 total tags in treatment: 14955747 INFO @ Sat, 03 Apr 2021 06:50:48: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:50:48: #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 06:50:48: #1 tags after filtering in treatment: 9952410 INFO @ Sat, 03 Apr 2021 06:50:48: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 03 Apr 2021 06:50:48: #1 finished! INFO @ Sat, 03 Apr 2021 06:50:48: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:50:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:50:49: #2 number of paired peaks: 805 WARNING @ Sat, 03 Apr 2021 06:50:49: Fewer paired peaks (805) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 805 pairs to build model! INFO @ Sat, 03 Apr 2021 06:50:49: start model_add_line... INFO @ Sat, 03 Apr 2021 06:50:49: start X-correlation... INFO @ Sat, 03 Apr 2021 06:50:49: end of X-cor INFO @ Sat, 03 Apr 2021 06:50:49: #2 finished! INFO @ Sat, 03 Apr 2021 06:50:49: #2 predicted fragment length is 113 bps INFO @ Sat, 03 Apr 2021 06:50:49: #2 alternative fragment length(s) may be 113 bps INFO @ Sat, 03 Apr 2021 06:50:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3029122/SRX3029122.10_model.r WARNING @ Sat, 03 Apr 2021 06:50:49: #2 Since the d (113) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:50:49: #2 You may need to consider one of the other alternative d(s): 113 WARNING @ Sat, 03 Apr 2021 06:50:49: #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 06:50:49: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:50:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:50:50: 31000000 INFO @ Sat, 03 Apr 2021 06:50:56: 32000000 INFO @ Sat, 03 Apr 2021 06:51:01: 33000000 INFO @ Sat, 03 Apr 2021 06:51:06: 34000000 INFO @ Sat, 03 Apr 2021 06:51:09: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:51:12: 35000000 INFO @ Sat, 03 Apr 2021 06:51:17: 36000000 INFO @ Sat, 03 Apr 2021 06:51:19: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 06:51:19: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 06:51:19: #1 total tags in treatment: 14955747 INFO @ Sat, 03 Apr 2021 06:51:19: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:51:19: #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 06:51:19: #1 tags after filtering in treatment: 9952410 INFO @ Sat, 03 Apr 2021 06:51:19: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 03 Apr 2021 06:51:19: #1 finished! INFO @ Sat, 03 Apr 2021 06:51:19: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:51:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:51:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3029122/SRX3029122.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:51:20: #2 number of paired peaks: 805 WARNING @ Sat, 03 Apr 2021 06:51:20: Fewer paired peaks (805) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 805 pairs to build model! INFO @ Sat, 03 Apr 2021 06:51:20: start model_add_line... INFO @ Sat, 03 Apr 2021 06:51:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3029122/SRX3029122.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:51:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3029122/SRX3029122.10_summits.bed INFO @ Sat, 03 Apr 2021 06:51:20: start X-correlation... INFO @ Sat, 03 Apr 2021 06:51:20: end of X-cor INFO @ Sat, 03 Apr 2021 06:51:20: #2 finished! INFO @ Sat, 03 Apr 2021 06:51:20: #2 predicted fragment length is 113 bps INFO @ Sat, 03 Apr 2021 06:51:20: #2 alternative fragment length(s) may be 113 bps INFO @ Sat, 03 Apr 2021 06:51:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3029122/SRX3029122.20_model.r INFO @ Sat, 03 Apr 2021 06:51:20: Done! WARNING @ Sat, 03 Apr 2021 06:51:20: #2 Since the d (113) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:51:20: #2 You may need to consider one of the other alternative d(s): 113 WARNING @ Sat, 03 Apr 2021 06:51:20: #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 06:51:20: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:51:20: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6351 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:51:39: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:51:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3029122/SRX3029122.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:51:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3029122/SRX3029122.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:51:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3029122/SRX3029122.20_summits.bed INFO @ Sat, 03 Apr 2021 06:51:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3231 records, 4 fields): 5 millis CompletedMACS2peakCalling