Job ID = 16432958 SRX = SRX13336908 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 22465377 spots for SRR17152880/SRR17152880.sra Written 22465377 spots for SRR17152880/SRR17152880.sra fastq に変換しました。 bowtie でマッピング中... Your job 16435034 ("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: 00:54:04 22465377 reads; of these: 22465377 (100.00%) were paired; of these: 13268021 (59.06%) aligned concordantly 0 times 7657998 (34.09%) aligned concordantly exactly 1 time 1539358 (6.85%) aligned concordantly >1 times ---- 13268021 pairs aligned concordantly 0 times; of these: 5711711 (43.05%) aligned discordantly 1 time ---- 7556310 pairs aligned 0 times concordantly or discordantly; of these: 15112620 mates make up the pairs; of these: 12682006 (83.92%) aligned 0 times 1240950 (8.21%) aligned exactly 1 time 1189664 (7.87%) aligned >1 times 71.77% overall alignment rate Time searching: 00:54:04 Overall time: 00:54:04 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 24 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] 1247956 / 14875923 = 0.0839 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 10:53:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13336908/SRX13336908.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13336908/SRX13336908.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13336908/SRX13336908.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13336908/SRX13336908.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 10:53:13: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:53:13: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:53:27: 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 10:53:41: 2000000 INFO @ Tue, 02 Aug 2022 10:53:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13336908/SRX13336908.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13336908/SRX13336908.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13336908/SRX13336908.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13336908/SRX13336908.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 10:53:42: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:53:42: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:53:55: 3000000 INFO @ Tue, 02 Aug 2022 10:53:56: 1000000 INFO @ Tue, 02 Aug 2022 10:54:09: 4000000 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 10:54:10: 2000000 INFO @ Tue, 02 Aug 2022 10:54:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13336908/SRX13336908.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13336908/SRX13336908.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13336908/SRX13336908.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13336908/SRX13336908.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 10:54:12: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:54:12: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:54:23: 5000000 INFO @ Tue, 02 Aug 2022 10:54:24: 3000000 INFO @ Tue, 02 Aug 2022 10:54:26: 1000000 INFO @ Tue, 02 Aug 2022 10:54:37: 6000000 INFO @ Tue, 02 Aug 2022 10:54:38: 4000000 INFO @ Tue, 02 Aug 2022 10:54:40: 2000000 INFO @ Tue, 02 Aug 2022 10:54:51: 7000000 INFO @ Tue, 02 Aug 2022 10:54:52: 5000000 INFO @ Tue, 02 Aug 2022 10:54:54: 3000000 INFO @ Tue, 02 Aug 2022 10:55:06: 8000000 INFO @ Tue, 02 Aug 2022 10:55:06: 6000000 INFO @ Tue, 02 Aug 2022 10:55:09: 4000000 INFO @ Tue, 02 Aug 2022 10:55:20: 7000000 INFO @ Tue, 02 Aug 2022 10:55:20: 9000000 INFO @ Tue, 02 Aug 2022 10:55:23: 5000000 INFO @ Tue, 02 Aug 2022 10:55:34: 8000000 INFO @ Tue, 02 Aug 2022 10:55:34: 10000000 INFO @ Tue, 02 Aug 2022 10:55:37: 6000000 INFO @ Tue, 02 Aug 2022 10:55:48: 9000000 INFO @ Tue, 02 Aug 2022 10:55:48: 11000000 INFO @ Tue, 02 Aug 2022 10:55:51: 7000000 INFO @ Tue, 02 Aug 2022 10:56:02: 10000000 INFO @ Tue, 02 Aug 2022 10:56:02: 12000000 INFO @ Tue, 02 Aug 2022 10:56:06: 8000000 INFO @ Tue, 02 Aug 2022 10:56:15: 11000000 INFO @ Tue, 02 Aug 2022 10:56:16: 13000000 INFO @ Tue, 02 Aug 2022 10:56:20: 9000000 INFO @ Tue, 02 Aug 2022 10:56:29: 12000000 INFO @ Tue, 02 Aug 2022 10:56:30: 14000000 INFO @ Tue, 02 Aug 2022 10:56:34: 10000000 INFO @ Tue, 02 Aug 2022 10:56:43: 13000000 INFO @ Tue, 02 Aug 2022 10:56:44: 15000000 INFO @ Tue, 02 Aug 2022 10:56:49: 11000000 INFO @ Tue, 02 Aug 2022 10:56:57: 14000000 INFO @ Tue, 02 Aug 2022 10:56:58: 16000000 INFO @ Tue, 02 Aug 2022 10:57:03: 12000000 INFO @ Tue, 02 Aug 2022 10:57:10: 15000000 INFO @ Tue, 02 Aug 2022 10:57:12: 17000000 INFO @ Tue, 02 Aug 2022 10:57:17: 13000000 INFO @ Tue, 02 Aug 2022 10:57:24: 16000000 INFO @ Tue, 02 Aug 2022 10:57:26: 18000000 INFO @ Tue, 02 Aug 2022 10:57:31: 14000000 INFO @ Tue, 02 Aug 2022 10:57:38: 17000000 INFO @ Tue, 02 Aug 2022 10:57:41: 19000000 INFO @ Tue, 02 Aug 2022 10:57:45: 15000000 INFO @ Tue, 02 Aug 2022 10:57:52: 18000000 INFO @ Tue, 02 Aug 2022 10:57:55: 20000000 INFO @ Tue, 02 Aug 2022 10:57:59: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:58:06: 19000000 INFO @ Tue, 02 Aug 2022 10:58:09: 21000000 INFO @ Tue, 02 Aug 2022 10:58:13: 17000000 INFO @ Tue, 02 Aug 2022 10:58:20: 20000000 INFO @ Tue, 02 Aug 2022 10:58:23: 22000000 INFO @ Tue, 02 Aug 2022 10:58:27: 18000000 INFO @ Tue, 02 Aug 2022 10:58:34: 21000000 INFO @ Tue, 02 Aug 2022 10:58:38: 23000000 INFO @ Tue, 02 Aug 2022 10:58:41: 19000000 INFO @ Tue, 02 Aug 2022 10:58:48: 22000000 INFO @ Tue, 02 Aug 2022 10:58:52: 24000000 INFO @ Tue, 02 Aug 2022 10:58:55: 20000000 INFO @ Tue, 02 Aug 2022 10:59:02: 23000000 INFO @ Tue, 02 Aug 2022 10:59:06: 25000000 INFO @ Tue, 02 Aug 2022 10:59:09: 21000000 INFO @ Tue, 02 Aug 2022 10:59:16: 24000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:59:21: 26000000 INFO @ Tue, 02 Aug 2022 10:59:24: 22000000 INFO @ Tue, 02 Aug 2022 10:59:30: 25000000 INFO @ Tue, 02 Aug 2022 10:59:35: 27000000 INFO @ Tue, 02 Aug 2022 10:59:38: 23000000 INFO @ Tue, 02 Aug 2022 10:59:44: 26000000 INFO @ Tue, 02 Aug 2022 10:59:49: 28000000 INFO @ Tue, 02 Aug 2022 10:59:52: 24000000 INFO @ Tue, 02 Aug 2022 10:59:57: 27000000 INFO @ Tue, 02 Aug 2022 11:00:03: 29000000 INFO @ Tue, 02 Aug 2022 11:00:06: 25000000 INFO @ Tue, 02 Aug 2022 11:00:11: 28000000 INFO @ Tue, 02 Aug 2022 11:00:14: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:00:14: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:00:14: #1 total tags in treatment: 8323392 INFO @ Tue, 02 Aug 2022 11:00:14: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:00:14: #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 11:00:14: #1 tags after filtering in treatment: 7601384 INFO @ Tue, 02 Aug 2022 11:00:14: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 02 Aug 2022 11:00:14: #1 finished! INFO @ Tue, 02 Aug 2022 11:00:14: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:00:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:00:15: #2 number of paired peaks: 577 WARNING @ Tue, 02 Aug 2022 11:00:15: Fewer paired peaks (577) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 577 pairs to build model! INFO @ Tue, 02 Aug 2022 11:00:15: start model_add_line... INFO @ Tue, 02 Aug 2022 11:00:15: start X-correlation... INFO @ Tue, 02 Aug 2022 11:00:15: end of X-cor INFO @ Tue, 02 Aug 2022 11:00:15: #2 finished! INFO @ Tue, 02 Aug 2022 11:00:15: #2 predicted fragment length is 229 bps INFO @ Tue, 02 Aug 2022 11:00:15: #2 alternative fragment length(s) may be 229 bps INFO @ Tue, 02 Aug 2022 11:00:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13336908/SRX13336908.05_model.r WARNING @ Tue, 02 Aug 2022 11:00:15: #2 Since the d (229) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:00:15: #2 You may need to consider one of the other alternative d(s): 229 WARNING @ Tue, 02 Aug 2022 11:00:15: #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 11:00:15: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:00:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:00:20: 26000000 INFO @ Tue, 02 Aug 2022 11:00:24: 29000000 INFO @ Tue, 02 Aug 2022 11:00:33: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:00:34: 27000000 INFO @ Tue, 02 Aug 2022 11:00:34: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:00:34: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:00:34: #1 total tags in treatment: 8323392 INFO @ Tue, 02 Aug 2022 11:00:34: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:00:34: #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 11:00:35: #1 tags after filtering in treatment: 7601384 INFO @ Tue, 02 Aug 2022 11:00:35: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 02 Aug 2022 11:00:35: #1 finished! INFO @ Tue, 02 Aug 2022 11:00:35: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:00:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:00:35: #2 number of paired peaks: 577 WARNING @ Tue, 02 Aug 2022 11:00:35: Fewer paired peaks (577) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 577 pairs to build model! INFO @ Tue, 02 Aug 2022 11:00:35: start model_add_line... INFO @ Tue, 02 Aug 2022 11:00:35: start X-correlation... INFO @ Tue, 02 Aug 2022 11:00:35: end of X-cor INFO @ Tue, 02 Aug 2022 11:00:35: #2 finished! INFO @ Tue, 02 Aug 2022 11:00:35: #2 predicted fragment length is 229 bps INFO @ Tue, 02 Aug 2022 11:00:35: #2 alternative fragment length(s) may be 229 bps INFO @ Tue, 02 Aug 2022 11:00:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13336908/SRX13336908.10_model.r WARNING @ Tue, 02 Aug 2022 11:00:35: #2 Since the d (229) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:00:35: #2 You may need to consider one of the other alternative d(s): 229 WARNING @ Tue, 02 Aug 2022 11:00:35: #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 11:00:35: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:00:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:00:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13336908/SRX13336908.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:00:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13336908/SRX13336908.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:00:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13336908/SRX13336908.05_summits.bed INFO @ Tue, 02 Aug 2022 11:00:40: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (487 records, 4 fields): 62 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:00:48: 28000000 INFO @ Tue, 02 Aug 2022 11:00:53: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:01:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13336908/SRX13336908.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:01:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13336908/SRX13336908.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:01:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13336908/SRX13336908.10_summits.bed INFO @ Tue, 02 Aug 2022 11:01:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (377 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:01:01: 29000000 INFO @ Tue, 02 Aug 2022 11:01:11: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:01:11: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:01:11: #1 total tags in treatment: 8323392 INFO @ Tue, 02 Aug 2022 11:01:11: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:01:11: #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 11:01:12: #1 tags after filtering in treatment: 7601384 INFO @ Tue, 02 Aug 2022 11:01:12: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 02 Aug 2022 11:01:12: #1 finished! INFO @ Tue, 02 Aug 2022 11:01:12: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:01:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:01:12: #2 number of paired peaks: 577 WARNING @ Tue, 02 Aug 2022 11:01:12: Fewer paired peaks (577) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 577 pairs to build model! INFO @ Tue, 02 Aug 2022 11:01:12: start model_add_line... INFO @ Tue, 02 Aug 2022 11:01:12: start X-correlation... INFO @ Tue, 02 Aug 2022 11:01:12: end of X-cor INFO @ Tue, 02 Aug 2022 11:01:12: #2 finished! INFO @ Tue, 02 Aug 2022 11:01:12: #2 predicted fragment length is 229 bps INFO @ Tue, 02 Aug 2022 11:01:12: #2 alternative fragment length(s) may be 229 bps INFO @ Tue, 02 Aug 2022 11:01:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13336908/SRX13336908.20_model.r WARNING @ Tue, 02 Aug 2022 11:01:12: #2 Since the d (229) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:01:12: #2 You may need to consider one of the other alternative d(s): 229 WARNING @ Tue, 02 Aug 2022 11:01:12: #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 11:01:12: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:01:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:01:30: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:01:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13336908/SRX13336908.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:01:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13336908/SRX13336908.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:01:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13336908/SRX13336908.20_summits.bed INFO @ Tue, 02 Aug 2022 11:01:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (285 records, 4 fields): 20 millis CompletedMACS2peakCalling