Job ID = 16432928 SRX = SRX13336906 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 24526602 spots for SRR17152882/SRR17152882.sra Written 24526602 spots for SRR17152882/SRR17152882.sra fastq に変換しました。 bowtie でマッピング中... Your job 16435248 ("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: 00:59:53 24526602 reads; of these: 24526602 (100.00%) were paired; of these: 12540770 (51.13%) aligned concordantly 0 times 10074135 (41.07%) aligned concordantly exactly 1 time 1911697 (7.79%) aligned concordantly >1 times ---- 12540770 pairs aligned concordantly 0 times; of these: 5577588 (44.48%) aligned discordantly 1 time ---- 6963182 pairs aligned 0 times concordantly or discordantly; of these: 13926364 mates make up the pairs; of these: 11773813 (84.54%) aligned 0 times 1015651 (7.29%) aligned exactly 1 time 1136900 (8.16%) aligned >1 times 76.00% overall alignment rate Time searching: 00:59:53 Overall time: 00:59:53 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 28 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] 1580001 / 17510908 = 0.0902 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:00:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13336906/SRX13336906.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13336906/SRX13336906.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13336906/SRX13336906.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13336906/SRX13336906.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 @ Tue, 02 Aug 2022 11:00:34: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:00:34: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:00:43: 1000000 INFO @ Tue, 02 Aug 2022 11:00:51: 2000000 INFO @ Tue, 02 Aug 2022 11:01:00: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:01:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13336906/SRX13336906.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13336906/SRX13336906.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13336906/SRX13336906.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13336906/SRX13336906.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 @ Tue, 02 Aug 2022 11:01:04: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:01:04: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:01:08: 4000000 INFO @ Tue, 02 Aug 2022 11:01:14: 1000000 INFO @ Tue, 02 Aug 2022 11:01:18: 5000000 INFO @ Tue, 02 Aug 2022 11:01:24: 2000000 INFO @ Tue, 02 Aug 2022 11:01:29: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 11:01:34: 3000000 INFO @ Tue, 02 Aug 2022 11:01:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13336906/SRX13336906.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13336906/SRX13336906.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13336906/SRX13336906.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13336906/SRX13336906.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 @ Tue, 02 Aug 2022 11:01:34: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:01:34: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:01:39: 7000000 INFO @ Tue, 02 Aug 2022 11:01:44: 4000000 INFO @ Tue, 02 Aug 2022 11:01:44: 1000000 INFO @ Tue, 02 Aug 2022 11:01:50: 8000000 INFO @ Tue, 02 Aug 2022 11:01:54: 2000000 INFO @ Tue, 02 Aug 2022 11:01:54: 5000000 INFO @ Tue, 02 Aug 2022 11:02:02: 9000000 INFO @ Tue, 02 Aug 2022 11:02:03: 3000000 INFO @ Tue, 02 Aug 2022 11:02:06: 6000000 INFO @ Tue, 02 Aug 2022 11:02:13: 4000000 INFO @ Tue, 02 Aug 2022 11:02:14: 10000000 INFO @ Tue, 02 Aug 2022 11:02:17: 7000000 INFO @ Tue, 02 Aug 2022 11:02:23: 5000000 INFO @ Tue, 02 Aug 2022 11:02:26: 11000000 INFO @ Tue, 02 Aug 2022 11:02:29: 8000000 INFO @ Tue, 02 Aug 2022 11:02:34: 6000000 INFO @ Tue, 02 Aug 2022 11:02:38: 12000000 INFO @ Tue, 02 Aug 2022 11:02:41: 9000000 INFO @ Tue, 02 Aug 2022 11:02:45: 7000000 INFO @ Tue, 02 Aug 2022 11:02:51: 13000000 INFO @ Tue, 02 Aug 2022 11:02:53: 10000000 INFO @ Tue, 02 Aug 2022 11:02:56: 8000000 INFO @ Tue, 02 Aug 2022 11:03:04: 14000000 INFO @ Tue, 02 Aug 2022 11:03:06: 9000000 INFO @ Tue, 02 Aug 2022 11:03:06: 11000000 INFO @ Tue, 02 Aug 2022 11:03:16: 15000000 INFO @ Tue, 02 Aug 2022 11:03:17: 10000000 INFO @ Tue, 02 Aug 2022 11:03:20: 12000000 INFO @ Tue, 02 Aug 2022 11:03:28: 11000000 INFO @ Tue, 02 Aug 2022 11:03:30: 16000000 INFO @ Tue, 02 Aug 2022 11:03:34: 13000000 INFO @ Tue, 02 Aug 2022 11:03:39: 12000000 INFO @ Tue, 02 Aug 2022 11:03:43: 17000000 INFO @ Tue, 02 Aug 2022 11:03:48: 13000000 INFO @ Tue, 02 Aug 2022 11:03:49: 14000000 INFO @ Tue, 02 Aug 2022 11:03:55: 18000000 INFO @ Tue, 02 Aug 2022 11:03:59: 14000000 INFO @ Tue, 02 Aug 2022 11:04:02: 15000000 INFO @ Tue, 02 Aug 2022 11:04:08: 19000000 INFO @ Tue, 02 Aug 2022 11:04:09: 15000000 INFO @ Tue, 02 Aug 2022 11:04:15: 16000000 INFO @ Tue, 02 Aug 2022 11:04:19: 16000000 INFO @ Tue, 02 Aug 2022 11:04:21: 20000000 INFO @ Tue, 02 Aug 2022 11:04:28: 17000000 INFO @ Tue, 02 Aug 2022 11:04:29: 17000000 INFO @ Tue, 02 Aug 2022 11:04:34: 21000000 INFO @ Tue, 02 Aug 2022 11:04:39: 18000000 INFO @ Tue, 02 Aug 2022 11:04:40: 18000000 INFO @ Tue, 02 Aug 2022 11:04:47: 22000000 INFO @ Tue, 02 Aug 2022 11:04:49: 19000000 INFO @ Tue, 02 Aug 2022 11:04:53: 19000000 INFO @ Tue, 02 Aug 2022 11:04:59: 23000000 INFO @ Tue, 02 Aug 2022 11:05:00: 20000000 INFO @ Tue, 02 Aug 2022 11:05:06: 20000000 INFO @ Tue, 02 Aug 2022 11:05:10: 21000000 INFO @ Tue, 02 Aug 2022 11:05:12: 24000000 INFO @ Tue, 02 Aug 2022 11:05:18: 21000000 INFO @ Tue, 02 Aug 2022 11:05:22: 22000000 INFO @ Tue, 02 Aug 2022 11:05:24: 25000000 INFO @ Tue, 02 Aug 2022 11:05:30: 22000000 INFO @ Tue, 02 Aug 2022 11:05:32: 23000000 INFO @ Tue, 02 Aug 2022 11:05:36: 26000000 INFO @ Tue, 02 Aug 2022 11:05:41: 24000000 INFO @ Tue, 02 Aug 2022 11:05:42: 23000000 INFO @ Tue, 02 Aug 2022 11:05:48: 27000000 INFO @ Tue, 02 Aug 2022 11:05:51: 25000000 INFO @ Tue, 02 Aug 2022 11:05:55: 24000000 INFO @ Tue, 02 Aug 2022 11:06:01: 28000000 INFO @ Tue, 02 Aug 2022 11:06:01: 26000000 INFO @ Tue, 02 Aug 2022 11:06:07: 25000000 INFO @ Tue, 02 Aug 2022 11:06:11: 27000000 INFO @ Tue, 02 Aug 2022 11:06:13: 29000000 INFO @ Tue, 02 Aug 2022 11:06:19: 26000000 INFO @ Tue, 02 Aug 2022 11:06:21: 28000000 INFO @ Tue, 02 Aug 2022 11:06:26: 30000000 INFO @ Tue, 02 Aug 2022 11:06:30: 29000000 INFO @ Tue, 02 Aug 2022 11:06:31: 27000000 INFO @ Tue, 02 Aug 2022 11:06:38: 31000000 INFO @ Tue, 02 Aug 2022 11:06:40: 30000000 INFO @ Tue, 02 Aug 2022 11:06:43: 28000000 INFO @ Tue, 02 Aug 2022 11:06:49: 31000000 INFO @ Tue, 02 Aug 2022 11:06:51: 32000000 INFO @ Tue, 02 Aug 2022 11:06:56: 29000000 INFO @ Tue, 02 Aug 2022 11:06:58: 32000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:07:03: 33000000 INFO @ Tue, 02 Aug 2022 11:07:08: 33000000 INFO @ Tue, 02 Aug 2022 11:07:08: 30000000 INFO @ Tue, 02 Aug 2022 11:07:15: 34000000 INFO @ Tue, 02 Aug 2022 11:07:17: 34000000 INFO @ Tue, 02 Aug 2022 11:07:17: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:07:17: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:07:17: #1 total tags in treatment: 10792188 INFO @ Tue, 02 Aug 2022 11:07:17: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:07:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:07:17: #1 tags after filtering in treatment: 9828120 INFO @ Tue, 02 Aug 2022 11:07:17: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 02 Aug 2022 11:07:17: #1 finished! INFO @ Tue, 02 Aug 2022 11:07:17: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:07:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:07:18: #2 number of paired peaks: 495 WARNING @ Tue, 02 Aug 2022 11:07:18: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Tue, 02 Aug 2022 11:07:18: start model_add_line... INFO @ Tue, 02 Aug 2022 11:07:18: start X-correlation... INFO @ Tue, 02 Aug 2022 11:07:18: end of X-cor INFO @ Tue, 02 Aug 2022 11:07:18: #2 finished! INFO @ Tue, 02 Aug 2022 11:07:18: #2 predicted fragment length is 221 bps INFO @ Tue, 02 Aug 2022 11:07:18: #2 alternative fragment length(s) may be 221 bps INFO @ Tue, 02 Aug 2022 11:07:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13336906/SRX13336906.05_model.r WARNING @ Tue, 02 Aug 2022 11:07:18: #2 Since the d (221) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:07:18: #2 You may need to consider one of the other alternative d(s): 221 WARNING @ Tue, 02 Aug 2022 11:07:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 11:07:18: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:07:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:07:18: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:07:18: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:07:18: #1 total tags in treatment: 10792188 INFO @ Tue, 02 Aug 2022 11:07:18: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:07:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:07:19: #1 tags after filtering in treatment: 9828120 INFO @ Tue, 02 Aug 2022 11:07:19: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 02 Aug 2022 11:07:19: #1 finished! INFO @ Tue, 02 Aug 2022 11:07:19: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:07:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:07:19: #2 number of paired peaks: 495 WARNING @ Tue, 02 Aug 2022 11:07:19: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Tue, 02 Aug 2022 11:07:19: start model_add_line... INFO @ Tue, 02 Aug 2022 11:07:19: start X-correlation... INFO @ Tue, 02 Aug 2022 11:07:19: end of X-cor INFO @ Tue, 02 Aug 2022 11:07:19: #2 finished! INFO @ Tue, 02 Aug 2022 11:07:19: #2 predicted fragment length is 221 bps INFO @ Tue, 02 Aug 2022 11:07:19: #2 alternative fragment length(s) may be 221 bps INFO @ Tue, 02 Aug 2022 11:07:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13336906/SRX13336906.20_model.r WARNING @ Tue, 02 Aug 2022 11:07:19: #2 Since the d (221) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:07:19: #2 You may need to consider one of the other alternative d(s): 221 WARNING @ Tue, 02 Aug 2022 11:07:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 11:07:19: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:07:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:07:20: 31000000 INFO @ Tue, 02 Aug 2022 11:07:33: 32000000 INFO @ Tue, 02 Aug 2022 11:07:40: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:07:41: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:07:45: 33000000 INFO @ Tue, 02 Aug 2022 11:07:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13336906/SRX13336906.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:07:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13336906/SRX13336906.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:07:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13336906/SRX13336906.05_summits.bed INFO @ Tue, 02 Aug 2022 11:07:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (513 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:07:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13336906/SRX13336906.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:07:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13336906/SRX13336906.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:07:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13336906/SRX13336906.20_summits.bed INFO @ Tue, 02 Aug 2022 11:07:51: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (293 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:07:57: 34000000 INFO @ Tue, 02 Aug 2022 11:07:58: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:07:58: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:07:58: #1 total tags in treatment: 10792188 INFO @ Tue, 02 Aug 2022 11:07:58: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:07:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 11:07:58: #1 tags after filtering in treatment: 9828120 INFO @ Tue, 02 Aug 2022 11:07:58: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 02 Aug 2022 11:07:58: #1 finished! INFO @ Tue, 02 Aug 2022 11:07:58: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:07:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:07:59: #2 number of paired peaks: 495 WARNING @ Tue, 02 Aug 2022 11:07:59: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Tue, 02 Aug 2022 11:07:59: start model_add_line... INFO @ Tue, 02 Aug 2022 11:07:59: start X-correlation... INFO @ Tue, 02 Aug 2022 11:07:59: end of X-cor INFO @ Tue, 02 Aug 2022 11:07:59: #2 finished! INFO @ Tue, 02 Aug 2022 11:07:59: #2 predicted fragment length is 221 bps INFO @ Tue, 02 Aug 2022 11:07:59: #2 alternative fragment length(s) may be 221 bps INFO @ Tue, 02 Aug 2022 11:07:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13336906/SRX13336906.10_model.r WARNING @ Tue, 02 Aug 2022 11:07:59: #2 Since the d (221) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:07:59: #2 You may need to consider one of the other alternative d(s): 221 WARNING @ Tue, 02 Aug 2022 11:07:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 11:07:59: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:07:59: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:08:21: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:08:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13336906/SRX13336906.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:08:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13336906/SRX13336906.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:08:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13336906/SRX13336906.10_summits.bed INFO @ Tue, 02 Aug 2022 11:08:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (406 records, 4 fields): 17 millis CompletedMACS2peakCalling