Job ID = 12264758 SRX = SRX3029123 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 29483489 spots for SRR5860423/SRR5860423.sra Written 29483489 spots for SRR5860423/SRR5860423.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265403 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:33:09 29483489 reads; of these: 29483489 (100.00%) were paired; of these: 9136837 (30.99%) aligned concordantly 0 times 17992414 (61.03%) aligned concordantly exactly 1 time 2354238 (7.98%) aligned concordantly >1 times ---- 9136837 pairs aligned concordantly 0 times; of these: 2457496 (26.90%) aligned discordantly 1 time ---- 6679341 pairs aligned 0 times concordantly or discordantly; of these: 13358682 mates make up the pairs; of these: 12131642 (90.81%) aligned 0 times 582327 (4.36%) aligned exactly 1 time 644713 (4.83%) aligned >1 times 79.43% overall alignment rate Time searching: 00:33:10 Overall time: 00:33:10 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] 8301999 / 22612715 = 0.3671 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 06:49:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3029123/SRX3029123.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3029123/SRX3029123.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3029123/SRX3029123.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3029123/SRX3029123.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 06:49:42: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:49:42: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:49:50: 1000000 INFO @ Sat, 03 Apr 2021 06:49:58: 2000000 INFO @ Sat, 03 Apr 2021 06:50:06: 3000000 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 06:50:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3029123/SRX3029123.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3029123/SRX3029123.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3029123/SRX3029123.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3029123/SRX3029123.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 06:50:12: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:50:12: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:50:15: 4000000 INFO @ Sat, 03 Apr 2021 06:50:21: 1000000 INFO @ Sat, 03 Apr 2021 06:50:23: 5000000 INFO @ Sat, 03 Apr 2021 06:50:29: 2000000 INFO @ Sat, 03 Apr 2021 06:50:31: 6000000 INFO @ Sat, 03 Apr 2021 06:50:38: 3000000 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 06:50:40: 7000000 INFO @ Sat, 03 Apr 2021 06:50:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3029123/SRX3029123.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3029123/SRX3029123.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3029123/SRX3029123.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3029123/SRX3029123.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 06:50:42: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:50:42: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:50:46: 4000000 INFO @ Sat, 03 Apr 2021 06:50:48: 8000000 INFO @ Sat, 03 Apr 2021 06:50:51: 1000000 INFO @ Sat, 03 Apr 2021 06:50:55: 5000000 INFO @ Sat, 03 Apr 2021 06:50:57: 9000000 INFO @ Sat, 03 Apr 2021 06:51:00: 2000000 INFO @ Sat, 03 Apr 2021 06:51:04: 6000000 INFO @ Sat, 03 Apr 2021 06:51:05: 10000000 INFO @ Sat, 03 Apr 2021 06:51:09: 3000000 INFO @ Sat, 03 Apr 2021 06:51:13: 7000000 INFO @ Sat, 03 Apr 2021 06:51:14: 11000000 INFO @ Sat, 03 Apr 2021 06:51:19: 4000000 INFO @ Sat, 03 Apr 2021 06:51:21: 8000000 INFO @ Sat, 03 Apr 2021 06:51:22: 12000000 INFO @ Sat, 03 Apr 2021 06:51:28: 5000000 INFO @ Sat, 03 Apr 2021 06:51:31: 13000000 INFO @ Sat, 03 Apr 2021 06:51:31: 9000000 INFO @ Sat, 03 Apr 2021 06:51:38: 6000000 INFO @ Sat, 03 Apr 2021 06:51:39: 14000000 INFO @ Sat, 03 Apr 2021 06:51:40: 10000000 INFO @ Sat, 03 Apr 2021 06:51:47: 7000000 INFO @ Sat, 03 Apr 2021 06:51:48: 15000000 INFO @ Sat, 03 Apr 2021 06:51:50: 11000000 INFO @ Sat, 03 Apr 2021 06:51:58: 16000000 INFO @ Sat, 03 Apr 2021 06:51:59: 8000000 INFO @ Sat, 03 Apr 2021 06:52:02: 12000000 INFO @ Sat, 03 Apr 2021 06:52:10: 17000000 INFO @ Sat, 03 Apr 2021 06:52:10: 9000000 INFO @ Sat, 03 Apr 2021 06:52:12: 13000000 INFO @ Sat, 03 Apr 2021 06:52:19: 18000000 INFO @ Sat, 03 Apr 2021 06:52:21: 10000000 INFO @ Sat, 03 Apr 2021 06:52:24: 14000000 INFO @ Sat, 03 Apr 2021 06:52:29: 19000000 INFO @ Sat, 03 Apr 2021 06:52:33: 11000000 INFO @ Sat, 03 Apr 2021 06:52:36: 15000000 INFO @ Sat, 03 Apr 2021 06:52:39: 20000000 INFO @ Sat, 03 Apr 2021 06:52:45: 12000000 INFO @ Sat, 03 Apr 2021 06:52:48: 16000000 INFO @ Sat, 03 Apr 2021 06:52:48: 21000000 INFO @ Sat, 03 Apr 2021 06:52:58: 13000000 INFO @ Sat, 03 Apr 2021 06:52:58: 22000000 INFO @ Sat, 03 Apr 2021 06:52:59: 17000000 INFO @ Sat, 03 Apr 2021 06:53:08: 23000000 INFO @ Sat, 03 Apr 2021 06:53:10: 18000000 INFO @ Sat, 03 Apr 2021 06:53:11: 14000000 INFO @ Sat, 03 Apr 2021 06:53:19: 24000000 INFO @ Sat, 03 Apr 2021 06:53:21: 19000000 INFO @ Sat, 03 Apr 2021 06:53:22: 15000000 INFO @ Sat, 03 Apr 2021 06:53:33: 20000000 INFO @ Sat, 03 Apr 2021 06:53:33: 16000000 INFO @ Sat, 03 Apr 2021 06:53:35: 25000000 INFO @ Sat, 03 Apr 2021 06:53:45: 17000000 INFO @ Sat, 03 Apr 2021 06:53:45: 21000000 INFO @ Sat, 03 Apr 2021 06:53:50: 26000000 INFO @ Sat, 03 Apr 2021 06:53:57: 18000000 INFO @ Sat, 03 Apr 2021 06:53:57: 22000000 INFO @ Sat, 03 Apr 2021 06:54:05: 27000000 INFO @ Sat, 03 Apr 2021 06:54:08: 19000000 INFO @ Sat, 03 Apr 2021 06:54:10: 23000000 INFO @ Sat, 03 Apr 2021 06:54:20: 28000000 INFO @ Sat, 03 Apr 2021 06:54:20: 20000000 INFO @ Sat, 03 Apr 2021 06:54:22: 24000000 INFO @ Sat, 03 Apr 2021 06:54:31: 21000000 INFO @ Sat, 03 Apr 2021 06:54:33: 25000000 INFO @ Sat, 03 Apr 2021 06:54:35: 29000000 INFO @ Sat, 03 Apr 2021 06:54:42: 22000000 INFO @ Sat, 03 Apr 2021 06:54:43: 26000000 INFO @ Sat, 03 Apr 2021 06:54:49: 30000000 INFO @ Sat, 03 Apr 2021 06:54:51: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 06:54:51: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 06:54:51: #1 total tags in treatment: 12854253 INFO @ Sat, 03 Apr 2021 06:54:51: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:54:51: #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 06:54:52: #1 tags after filtering in treatment: 8933966 INFO @ Sat, 03 Apr 2021 06:54:52: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 03 Apr 2021 06:54:52: #1 finished! INFO @ Sat, 03 Apr 2021 06:54:52: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:54:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:54:53: #2 number of paired peaks: 647 WARNING @ Sat, 03 Apr 2021 06:54:53: Fewer paired peaks (647) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 647 pairs to build model! INFO @ Sat, 03 Apr 2021 06:54:53: start model_add_line... INFO @ Sat, 03 Apr 2021 06:54:53: start X-correlation... INFO @ Sat, 03 Apr 2021 06:54:53: end of X-cor INFO @ Sat, 03 Apr 2021 06:54:53: #2 finished! INFO @ Sat, 03 Apr 2021 06:54:53: #2 predicted fragment length is 127 bps INFO @ Sat, 03 Apr 2021 06:54:53: #2 alternative fragment length(s) may be 127 bps INFO @ Sat, 03 Apr 2021 06:54:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3029123/SRX3029123.05_model.r WARNING @ Sat, 03 Apr 2021 06:54:53: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:54:53: #2 You may need to consider one of the other alternative d(s): 127 WARNING @ Sat, 03 Apr 2021 06:54:53: #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 06:54:53: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:54:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:54:54: 23000000 INFO @ Sat, 03 Apr 2021 06:54:54: 27000000 INFO @ Sat, 03 Apr 2021 06:55:05: 24000000 INFO @ Sat, 03 Apr 2021 06:55:05: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:55:15: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:55:16: 29000000 INFO @ Sat, 03 Apr 2021 06:55:16: 25000000 INFO @ Sat, 03 Apr 2021 06:55:26: 30000000 INFO @ Sat, 03 Apr 2021 06:55:27: 26000000 INFO @ Sat, 03 Apr 2021 06:55:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3029123/SRX3029123.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:55:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3029123/SRX3029123.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:55:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3029123/SRX3029123.05_summits.bed INFO @ Sat, 03 Apr 2021 06:55:27: Done! pass1 - making usageList (7 chroms): 6 millis pass2 - checking and writing primary data (6563 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:55:28: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 06:55:28: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 06:55:28: #1 total tags in treatment: 12854253 INFO @ Sat, 03 Apr 2021 06:55:28: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:55:28: #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 06:55:29: #1 tags after filtering in treatment: 8933966 INFO @ Sat, 03 Apr 2021 06:55:29: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 03 Apr 2021 06:55:29: #1 finished! INFO @ Sat, 03 Apr 2021 06:55:29: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:55:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:55:30: #2 number of paired peaks: 647 WARNING @ Sat, 03 Apr 2021 06:55:30: Fewer paired peaks (647) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 647 pairs to build model! INFO @ Sat, 03 Apr 2021 06:55:30: start model_add_line... INFO @ Sat, 03 Apr 2021 06:55:30: start X-correlation... INFO @ Sat, 03 Apr 2021 06:55:30: end of X-cor INFO @ Sat, 03 Apr 2021 06:55:30: #2 finished! INFO @ Sat, 03 Apr 2021 06:55:30: #2 predicted fragment length is 127 bps INFO @ Sat, 03 Apr 2021 06:55:30: #2 alternative fragment length(s) may be 127 bps INFO @ Sat, 03 Apr 2021 06:55:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3029123/SRX3029123.10_model.r WARNING @ Sat, 03 Apr 2021 06:55:30: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:55:30: #2 You may need to consider one of the other alternative d(s): 127 WARNING @ Sat, 03 Apr 2021 06:55:30: #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 06:55:30: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:55:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:55:37: 27000000 INFO @ Sat, 03 Apr 2021 06:55:47: 28000000 INFO @ Sat, 03 Apr 2021 06:55:51: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:55:57: 29000000 INFO @ Sat, 03 Apr 2021 06:56:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3029123/SRX3029123.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:56:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3029123/SRX3029123.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:56:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3029123/SRX3029123.10_summits.bed INFO @ Sat, 03 Apr 2021 06:56:02: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3787 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:56:06: 30000000 INFO @ Sat, 03 Apr 2021 06:56:09: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 06:56:09: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 06:56:09: #1 total tags in treatment: 12854253 INFO @ Sat, 03 Apr 2021 06:56:09: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:56:09: #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 06:56:09: #1 tags after filtering in treatment: 8933966 INFO @ Sat, 03 Apr 2021 06:56:09: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 03 Apr 2021 06:56:09: #1 finished! INFO @ Sat, 03 Apr 2021 06:56:09: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:56:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:56:09: #2 number of paired peaks: 647 WARNING @ Sat, 03 Apr 2021 06:56:09: Fewer paired peaks (647) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 647 pairs to build model! INFO @ Sat, 03 Apr 2021 06:56:09: start model_add_line... INFO @ Sat, 03 Apr 2021 06:56:10: start X-correlation... INFO @ Sat, 03 Apr 2021 06:56:10: end of X-cor INFO @ Sat, 03 Apr 2021 06:56:10: #2 finished! INFO @ Sat, 03 Apr 2021 06:56:10: #2 predicted fragment length is 127 bps INFO @ Sat, 03 Apr 2021 06:56:10: #2 alternative fragment length(s) may be 127 bps INFO @ Sat, 03 Apr 2021 06:56:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3029123/SRX3029123.20_model.r WARNING @ Sat, 03 Apr 2021 06:56:10: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:56:10: #2 You may need to consider one of the other alternative d(s): 127 WARNING @ Sat, 03 Apr 2021 06:56:10: #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 06:56:10: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:56:10: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:56:30: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:56:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3029123/SRX3029123.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:56:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3029123/SRX3029123.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:56:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3029123/SRX3029123.20_summits.bed INFO @ Sat, 03 Apr 2021 06:56:40: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (1918 records, 4 fields): 10 millis CompletedMACS2peakCalling