Job ID = 16432953 SRX = SRX13336907 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 25559692 spots for SRR17152881/SRR17152881.sra Written 25559692 spots for SRR17152881/SRR17152881.sra fastq に変換しました。 bowtie でマッピング中... Your job 16435528 ("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: 01:05:31 25559692 reads; of these: 25559692 (100.00%) were paired; of these: 11186085 (43.76%) aligned concordantly 0 times 12263373 (47.98%) aligned concordantly exactly 1 time 2110234 (8.26%) aligned concordantly >1 times ---- 11186085 pairs aligned concordantly 0 times; of these: 4288200 (38.34%) aligned discordantly 1 time ---- 6897885 pairs aligned 0 times concordantly or discordantly; of these: 13795770 mates make up the pairs; of these: 12234574 (88.68%) aligned 0 times 715888 (5.19%) aligned exactly 1 time 845308 (6.13%) aligned >1 times 76.07% overall alignment rate Time searching: 01:05:31 Overall time: 01:05:31 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 32 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] 2631582 / 18580496 = 0.1416 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 11:06:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13336907/SRX13336907.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13336907/SRX13336907.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13336907/SRX13336907.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13336907/SRX13336907.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 11:06:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:06:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:06:37: 1000000 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 11:06:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13336907/SRX13336907.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13336907/SRX13336907.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13336907/SRX13336907.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13336907/SRX13336907.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 11:06:51: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:06:51: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:06:53: 2000000 INFO @ Tue, 02 Aug 2022 11:07:06: 1000000 INFO @ Tue, 02 Aug 2022 11:07:08: 3000000 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 11:07:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13336907/SRX13336907.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13336907/SRX13336907.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13336907/SRX13336907.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13336907/SRX13336907.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 11:07:21: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:07:21: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:07:21: 2000000 INFO @ Tue, 02 Aug 2022 11:07:23: 4000000 INFO @ Tue, 02 Aug 2022 11:07:35: 1000000 INFO @ Tue, 02 Aug 2022 11:07:36: 3000000 INFO @ Tue, 02 Aug 2022 11:07:39: 5000000 INFO @ Tue, 02 Aug 2022 11:07:50: 2000000 INFO @ Tue, 02 Aug 2022 11:07:51: 4000000 INFO @ Tue, 02 Aug 2022 11:07:55: 6000000 INFO @ Tue, 02 Aug 2022 11:08:04: 3000000 INFO @ Tue, 02 Aug 2022 11:08:05: 5000000 INFO @ Tue, 02 Aug 2022 11:08:11: 7000000 INFO @ Tue, 02 Aug 2022 11:08:18: 4000000 INFO @ Tue, 02 Aug 2022 11:08:20: 6000000 INFO @ Tue, 02 Aug 2022 11:08:26: 8000000 INFO @ Tue, 02 Aug 2022 11:08:33: 5000000 INFO @ Tue, 02 Aug 2022 11:08:35: 7000000 INFO @ Tue, 02 Aug 2022 11:08:41: 9000000 INFO @ Tue, 02 Aug 2022 11:08:48: 6000000 INFO @ Tue, 02 Aug 2022 11:08:51: 8000000 INFO @ Tue, 02 Aug 2022 11:08:57: 10000000 INFO @ Tue, 02 Aug 2022 11:09:03: 7000000 INFO @ Tue, 02 Aug 2022 11:09:07: 9000000 INFO @ Tue, 02 Aug 2022 11:09:13: 11000000 INFO @ Tue, 02 Aug 2022 11:09:17: 8000000 INFO @ Tue, 02 Aug 2022 11:09:23: 10000000 INFO @ Tue, 02 Aug 2022 11:09:28: 12000000 INFO @ Tue, 02 Aug 2022 11:09:31: 9000000 INFO @ Tue, 02 Aug 2022 11:09:38: 11000000 INFO @ Tue, 02 Aug 2022 11:09:43: 13000000 INFO @ Tue, 02 Aug 2022 11:09:45: 10000000 INFO @ Tue, 02 Aug 2022 11:09:53: 12000000 INFO @ Tue, 02 Aug 2022 11:09:59: 14000000 INFO @ Tue, 02 Aug 2022 11:09:59: 11000000 INFO @ Tue, 02 Aug 2022 11:10:09: 13000000 INFO @ Tue, 02 Aug 2022 11:10:13: 12000000 INFO @ Tue, 02 Aug 2022 11:10:14: 15000000 INFO @ Tue, 02 Aug 2022 11:10:24: 14000000 INFO @ Tue, 02 Aug 2022 11:10:27: 13000000 INFO @ Tue, 02 Aug 2022 11:10:29: 16000000 INFO @ Tue, 02 Aug 2022 11:10:39: 15000000 INFO @ Tue, 02 Aug 2022 11:10:41: 14000000 INFO @ Tue, 02 Aug 2022 11:10:45: 17000000 INFO @ Tue, 02 Aug 2022 11:10:54: 15000000 INFO @ Tue, 02 Aug 2022 11:10:55: 16000000 INFO @ Tue, 02 Aug 2022 11:11:00: 18000000 INFO @ Tue, 02 Aug 2022 11:11:08: 16000000 INFO @ Tue, 02 Aug 2022 11:11:10: 17000000 INFO @ Tue, 02 Aug 2022 11:11:15: 19000000 INFO @ Tue, 02 Aug 2022 11:11:21: 17000000 INFO @ Tue, 02 Aug 2022 11:11:25: 18000000 INFO @ Tue, 02 Aug 2022 11:11:31: 20000000 INFO @ Tue, 02 Aug 2022 11:11:34: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:11:40: 19000000 INFO @ Tue, 02 Aug 2022 11:11:46: 21000000 INFO @ Tue, 02 Aug 2022 11:11:48: 19000000 INFO @ Tue, 02 Aug 2022 11:11:55: 20000000 INFO @ Tue, 02 Aug 2022 11:12:01: 22000000 INFO @ Tue, 02 Aug 2022 11:12:02: 20000000 INFO @ Tue, 02 Aug 2022 11:12:11: 21000000 INFO @ Tue, 02 Aug 2022 11:12:16: 21000000 INFO @ Tue, 02 Aug 2022 11:12:17: 23000000 INFO @ Tue, 02 Aug 2022 11:12:27: 22000000 INFO @ Tue, 02 Aug 2022 11:12:30: 22000000 INFO @ Tue, 02 Aug 2022 11:12:33: 24000000 INFO @ Tue, 02 Aug 2022 11:12:42: 23000000 INFO @ Tue, 02 Aug 2022 11:12:44: 23000000 INFO @ Tue, 02 Aug 2022 11:12:48: 25000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:12:58: 24000000 INFO @ Tue, 02 Aug 2022 11:12:58: 24000000 INFO @ Tue, 02 Aug 2022 11:13:04: 26000000 INFO @ Tue, 02 Aug 2022 11:13:13: 25000000 INFO @ Tue, 02 Aug 2022 11:13:14: 25000000 INFO @ Tue, 02 Aug 2022 11:13:19: 27000000 INFO @ Tue, 02 Aug 2022 11:13:27: 26000000 INFO @ Tue, 02 Aug 2022 11:13:29: 26000000 INFO @ Tue, 02 Aug 2022 11:13:35: 28000000 INFO @ Tue, 02 Aug 2022 11:13:43: 27000000 INFO @ Tue, 02 Aug 2022 11:13:45: 27000000 INFO @ Tue, 02 Aug 2022 11:13:51: 29000000 INFO @ Tue, 02 Aug 2022 11:13:57: 28000000 INFO @ Tue, 02 Aug 2022 11:14:00: 28000000 INFO @ Tue, 02 Aug 2022 11:14:07: 30000000 INFO @ Tue, 02 Aug 2022 11:14:10: 29000000 INFO @ Tue, 02 Aug 2022 11:14:15: 29000000 INFO @ Tue, 02 Aug 2022 11:14:22: 31000000 INFO @ Tue, 02 Aug 2022 11:14:24: 30000000 INFO @ Tue, 02 Aug 2022 11:14:32: 30000000 INFO @ Tue, 02 Aug 2022 11:14:37: 31000000 INFO @ Tue, 02 Aug 2022 11:14:38: 32000000 INFO @ Tue, 02 Aug 2022 11:14:47: 31000000 INFO @ Tue, 02 Aug 2022 11:14:50: 32000000 INFO @ Tue, 02 Aug 2022 11:14:53: 33000000 INFO @ Tue, 02 Aug 2022 11:15:02: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:15:02: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:15:02: #1 total tags in treatment: 12231409 INFO @ Tue, 02 Aug 2022 11:15:02: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:15:02: #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 11:15:02: #1 tags after filtering in treatment: 11229458 INFO @ Tue, 02 Aug 2022 11:15:02: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 02 Aug 2022 11:15:02: #1 finished! INFO @ Tue, 02 Aug 2022 11:15:02: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:15:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:15:03: #2 number of paired peaks: 453 WARNING @ Tue, 02 Aug 2022 11:15:03: Fewer paired peaks (453) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 453 pairs to build model! INFO @ Tue, 02 Aug 2022 11:15:03: start model_add_line... INFO @ Tue, 02 Aug 2022 11:15:03: start X-correlation... INFO @ Tue, 02 Aug 2022 11:15:03: end of X-cor INFO @ Tue, 02 Aug 2022 11:15:03: #2 finished! INFO @ Tue, 02 Aug 2022 11:15:03: #2 predicted fragment length is 213 bps INFO @ Tue, 02 Aug 2022 11:15:03: #2 alternative fragment length(s) may be 213 bps INFO @ Tue, 02 Aug 2022 11:15:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13336907/SRX13336907.05_model.r WARNING @ Tue, 02 Aug 2022 11:15:03: #2 Since the d (213) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:15:03: #2 You may need to consider one of the other alternative d(s): 213 WARNING @ Tue, 02 Aug 2022 11:15:03: #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 11:15:03: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:15:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:15:03: 33000000 INFO @ Tue, 02 Aug 2022 11:15:04: 32000000 INFO @ Tue, 02 Aug 2022 11:15:11: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:15:11: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:15:11: #1 total tags in treatment: 12231409 INFO @ Tue, 02 Aug 2022 11:15:11: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:15:11: #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 11:15:12: #1 tags after filtering in treatment: 11229458 INFO @ Tue, 02 Aug 2022 11:15:12: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 02 Aug 2022 11:15:12: #1 finished! INFO @ Tue, 02 Aug 2022 11:15:12: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:15:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:15:13: #2 number of paired peaks: 453 WARNING @ Tue, 02 Aug 2022 11:15:13: Fewer paired peaks (453) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 453 pairs to build model! INFO @ Tue, 02 Aug 2022 11:15:13: start model_add_line... INFO @ Tue, 02 Aug 2022 11:15:13: start X-correlation... INFO @ Tue, 02 Aug 2022 11:15:13: end of X-cor INFO @ Tue, 02 Aug 2022 11:15:13: #2 finished! INFO @ Tue, 02 Aug 2022 11:15:13: #2 predicted fragment length is 213 bps INFO @ Tue, 02 Aug 2022 11:15:13: #2 alternative fragment length(s) may be 213 bps INFO @ Tue, 02 Aug 2022 11:15:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13336907/SRX13336907.20_model.r WARNING @ Tue, 02 Aug 2022 11:15:13: #2 Since the d (213) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:15:13: #2 You may need to consider one of the other alternative d(s): 213 WARNING @ Tue, 02 Aug 2022 11:15:13: #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 11:15:13: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:15:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:15:18: 33000000 INFO @ Tue, 02 Aug 2022 11:15:26: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:15:27: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:15:27: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:15:27: #1 total tags in treatment: 12231409 INFO @ Tue, 02 Aug 2022 11:15:27: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:15:27: #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 11:15:27: #1 tags after filtering in treatment: 11229458 INFO @ Tue, 02 Aug 2022 11:15:27: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 02 Aug 2022 11:15:27: #1 finished! INFO @ Tue, 02 Aug 2022 11:15:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:15:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:15:28: #2 number of paired peaks: 453 WARNING @ Tue, 02 Aug 2022 11:15:28: Fewer paired peaks (453) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 453 pairs to build model! INFO @ Tue, 02 Aug 2022 11:15:28: start model_add_line... INFO @ Tue, 02 Aug 2022 11:15:28: start X-correlation... INFO @ Tue, 02 Aug 2022 11:15:28: end of X-cor INFO @ Tue, 02 Aug 2022 11:15:28: #2 finished! INFO @ Tue, 02 Aug 2022 11:15:28: #2 predicted fragment length is 213 bps INFO @ Tue, 02 Aug 2022 11:15:28: #2 alternative fragment length(s) may be 213 bps INFO @ Tue, 02 Aug 2022 11:15:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13336907/SRX13336907.10_model.r WARNING @ Tue, 02 Aug 2022 11:15:28: #2 Since the d (213) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:15:28: #2 You may need to consider one of the other alternative d(s): 213 WARNING @ Tue, 02 Aug 2022 11:15:28: #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 11:15:28: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:15:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:15:36: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:15:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13336907/SRX13336907.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:15:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13336907/SRX13336907.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:15:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13336907/SRX13336907.05_summits.bed INFO @ Tue, 02 Aug 2022 11:15:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (482 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:15:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13336907/SRX13336907.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:15:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13336907/SRX13336907.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:15:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13336907/SRX13336907.20_summits.bed INFO @ Tue, 02 Aug 2022 11:15:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (270 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:15:51: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:16:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13336907/SRX13336907.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:16:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13336907/SRX13336907.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:16:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13336907/SRX13336907.10_summits.bed INFO @ Tue, 02 Aug 2022 11:16:02: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (386 records, 4 fields): 28 millis CompletedMACS2peakCalling