Job ID = 16433009 SRX = SRX13336899 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 24013535 spots for SRR17152889/SRR17152889.sra Written 24013535 spots for SRR17152889/SRR17152889.sra fastq に変換しました。 bowtie でマッピング中... Your job 16435433 ("srTce11") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:57:35 24013535 reads; of these: 24013535 (100.00%) were paired; of these: 12811546 (53.35%) aligned concordantly 0 times 9386691 (39.09%) aligned concordantly exactly 1 time 1815298 (7.56%) aligned concordantly >1 times ---- 12811546 pairs aligned concordantly 0 times; of these: 6235315 (48.67%) aligned discordantly 1 time ---- 6576231 pairs aligned 0 times concordantly or discordantly; of these: 13152462 mates make up the pairs; of these: 10770522 (81.89%) aligned 0 times 1120527 (8.52%) aligned exactly 1 time 1261413 (9.59%) aligned >1 times 77.57% overall alignment rate Time searching: 00:57:36 Overall time: 00:57:36 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] 2230040 / 17392938 = 0.1282 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 11:01:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13336899/SRX13336899.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13336899/SRX13336899.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13336899/SRX13336899.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13336899/SRX13336899.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 11:01:17: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:01:17: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:01:26: 1000000 INFO @ Tue, 02 Aug 2022 11:01:35: 2000000 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 11:01:43: 3000000 INFO @ Tue, 02 Aug 2022 11:01:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13336899/SRX13336899.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13336899/SRX13336899.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13336899/SRX13336899.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13336899/SRX13336899.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 11:01:46: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:01:46: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:01:53: 4000000 INFO @ Tue, 02 Aug 2022 11:01:56: 1000000 INFO @ Tue, 02 Aug 2022 11:02:02: 5000000 INFO @ Tue, 02 Aug 2022 11:02:06: 2000000 INFO @ Tue, 02 Aug 2022 11:02:12: 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 11:02:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13336899/SRX13336899.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13336899/SRX13336899.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13336899/SRX13336899.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13336899/SRX13336899.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 11:02:16: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:02:16: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:02:16: 3000000 INFO @ Tue, 02 Aug 2022 11:02:21: 7000000 INFO @ Tue, 02 Aug 2022 11:02:26: 1000000 INFO @ Tue, 02 Aug 2022 11:02:27: 4000000 INFO @ Tue, 02 Aug 2022 11:02:31: 8000000 INFO @ Tue, 02 Aug 2022 11:02:37: 2000000 INFO @ Tue, 02 Aug 2022 11:02:37: 5000000 INFO @ Tue, 02 Aug 2022 11:02:40: 9000000 INFO @ Tue, 02 Aug 2022 11:02:47: 3000000 INFO @ Tue, 02 Aug 2022 11:02:47: 6000000 INFO @ Tue, 02 Aug 2022 11:02:49: 10000000 INFO @ Tue, 02 Aug 2022 11:02:57: 4000000 INFO @ Tue, 02 Aug 2022 11:02:57: 7000000 INFO @ Tue, 02 Aug 2022 11:02:58: 11000000 INFO @ Tue, 02 Aug 2022 11:03:05: 12000000 INFO @ Tue, 02 Aug 2022 11:03:07: 5000000 INFO @ Tue, 02 Aug 2022 11:03:08: 8000000 INFO @ Tue, 02 Aug 2022 11:03:13: 13000000 INFO @ Tue, 02 Aug 2022 11:03:17: 6000000 INFO @ Tue, 02 Aug 2022 11:03:18: 9000000 INFO @ Tue, 02 Aug 2022 11:03:21: 14000000 INFO @ Tue, 02 Aug 2022 11:03:27: 7000000 INFO @ Tue, 02 Aug 2022 11:03:28: 10000000 INFO @ Tue, 02 Aug 2022 11:03:29: 15000000 INFO @ Tue, 02 Aug 2022 11:03:36: 16000000 INFO @ Tue, 02 Aug 2022 11:03:37: 8000000 INFO @ Tue, 02 Aug 2022 11:03:38: 11000000 INFO @ Tue, 02 Aug 2022 11:03:44: 17000000 INFO @ Tue, 02 Aug 2022 11:03:48: 9000000 INFO @ Tue, 02 Aug 2022 11:03:48: 12000000 INFO @ Tue, 02 Aug 2022 11:03:52: 18000000 INFO @ Tue, 02 Aug 2022 11:03:58: 10000000 INFO @ Tue, 02 Aug 2022 11:03:58: 13000000 INFO @ Tue, 02 Aug 2022 11:03:59: 19000000 INFO @ Tue, 02 Aug 2022 11:04:07: 20000000 INFO @ Tue, 02 Aug 2022 11:04:08: 11000000 INFO @ Tue, 02 Aug 2022 11:04:08: 14000000 INFO @ Tue, 02 Aug 2022 11:04:15: 21000000 INFO @ Tue, 02 Aug 2022 11:04:18: 12000000 INFO @ Tue, 02 Aug 2022 11:04:18: 15000000 INFO @ Tue, 02 Aug 2022 11:04:22: 22000000 INFO @ Tue, 02 Aug 2022 11:04:28: 13000000 INFO @ Tue, 02 Aug 2022 11:04:29: 16000000 INFO @ Tue, 02 Aug 2022 11:04:30: 23000000 INFO @ Tue, 02 Aug 2022 11:04:37: 24000000 INFO @ Tue, 02 Aug 2022 11:04:38: 14000000 INFO @ Tue, 02 Aug 2022 11:04:38: 17000000 INFO @ Tue, 02 Aug 2022 11:04:45: 25000000 INFO @ Tue, 02 Aug 2022 11:04:47: 15000000 INFO @ Tue, 02 Aug 2022 11:04:47: 18000000 INFO @ Tue, 02 Aug 2022 11:04:52: 26000000 INFO @ Tue, 02 Aug 2022 11:04:56: 16000000 INFO @ Tue, 02 Aug 2022 11:04:57: 19000000 INFO @ Tue, 02 Aug 2022 11:05:00: 27000000 INFO @ Tue, 02 Aug 2022 11:05:06: 17000000 INFO @ Tue, 02 Aug 2022 11:05:06: 20000000 INFO @ Tue, 02 Aug 2022 11:05:08: 28000000 INFO @ Tue, 02 Aug 2022 11:05:15: 18000000 INFO @ Tue, 02 Aug 2022 11:05:15: 21000000 INFO @ Tue, 02 Aug 2022 11:05:15: 29000000 INFO @ Tue, 02 Aug 2022 11:05:23: 30000000 INFO @ Tue, 02 Aug 2022 11:05:24: 19000000 INFO @ Tue, 02 Aug 2022 11:05:24: 22000000 INFO @ Tue, 02 Aug 2022 11:05:30: 31000000 INFO @ Tue, 02 Aug 2022 11:05:33: 20000000 INFO @ Tue, 02 Aug 2022 11:05:33: 23000000 INFO @ Tue, 02 Aug 2022 11:05:38: 32000000 INFO @ Tue, 02 Aug 2022 11:05:42: 21000000 INFO @ Tue, 02 Aug 2022 11:05:42: 24000000 INFO @ Tue, 02 Aug 2022 11:05:44: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:05:44: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:05:44: #1 total tags in treatment: 9649005 INFO @ Tue, 02 Aug 2022 11:05:44: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:05:44: #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 11:05:44: #1 tags after filtering in treatment: 8763941 INFO @ Tue, 02 Aug 2022 11:05:44: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 02 Aug 2022 11:05:44: #1 finished! INFO @ Tue, 02 Aug 2022 11:05:44: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:05:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:05:44: #2 number of paired peaks: 568 WARNING @ Tue, 02 Aug 2022 11:05:44: Fewer paired peaks (568) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 568 pairs to build model! INFO @ Tue, 02 Aug 2022 11:05:44: start model_add_line... INFO @ Tue, 02 Aug 2022 11:05:45: start X-correlation... INFO @ Tue, 02 Aug 2022 11:05:45: end of X-cor INFO @ Tue, 02 Aug 2022 11:05:45: #2 finished! INFO @ Tue, 02 Aug 2022 11:05:45: #2 predicted fragment length is 222 bps INFO @ Tue, 02 Aug 2022 11:05:45: #2 alternative fragment length(s) may be 222 bps INFO @ Tue, 02 Aug 2022 11:05:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13336899/SRX13336899.05_model.r WARNING @ Tue, 02 Aug 2022 11:05:45: #2 Since the d (222) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:05:45: #2 You may need to consider one of the other alternative d(s): 222 WARNING @ Tue, 02 Aug 2022 11:05:45: #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 11:05:45: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:05:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:05:51: 22000000 INFO @ Tue, 02 Aug 2022 11:05:51: 25000000 INFO @ Tue, 02 Aug 2022 11:06:00: 23000000 INFO @ Tue, 02 Aug 2022 11:06:00: 26000000 INFO @ Tue, 02 Aug 2022 11:06:04: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:06:08: 24000000 INFO @ Tue, 02 Aug 2022 11:06:09: 27000000 INFO @ Tue, 02 Aug 2022 11:06:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13336899/SRX13336899.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:06:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13336899/SRX13336899.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:06:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13336899/SRX13336899.05_summits.bed INFO @ Tue, 02 Aug 2022 11:06:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (500 records, 4 fields): 195 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:06:17: 25000000 INFO @ Tue, 02 Aug 2022 11:06:18: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:06:26: 26000000 INFO @ Tue, 02 Aug 2022 11:06:27: 29000000 INFO @ Tue, 02 Aug 2022 11:06:34: 30000000 INFO @ Tue, 02 Aug 2022 11:06:34: 27000000 INFO @ Tue, 02 Aug 2022 11:06:41: 31000000 INFO @ Tue, 02 Aug 2022 11:06:41: 28000000 INFO @ Tue, 02 Aug 2022 11:06:48: 32000000 INFO @ Tue, 02 Aug 2022 11:06:48: 29000000 INFO @ Tue, 02 Aug 2022 11:06:53: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:06:53: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:06:53: #1 total tags in treatment: 9649005 INFO @ Tue, 02 Aug 2022 11:06:53: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:06:53: #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 11:06:53: #1 tags after filtering in treatment: 8763941 INFO @ Tue, 02 Aug 2022 11:06:53: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 02 Aug 2022 11:06:53: #1 finished! INFO @ Tue, 02 Aug 2022 11:06:53: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:06:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:06:54: #2 number of paired peaks: 568 WARNING @ Tue, 02 Aug 2022 11:06:54: Fewer paired peaks (568) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 568 pairs to build model! INFO @ Tue, 02 Aug 2022 11:06:54: start model_add_line... INFO @ Tue, 02 Aug 2022 11:06:54: start X-correlation... INFO @ Tue, 02 Aug 2022 11:06:54: end of X-cor INFO @ Tue, 02 Aug 2022 11:06:54: #2 finished! INFO @ Tue, 02 Aug 2022 11:06:54: #2 predicted fragment length is 222 bps INFO @ Tue, 02 Aug 2022 11:06:54: #2 alternative fragment length(s) may be 222 bps INFO @ Tue, 02 Aug 2022 11:06:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13336899/SRX13336899.10_model.r WARNING @ Tue, 02 Aug 2022 11:06:54: #2 Since the d (222) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:06:54: #2 You may need to consider one of the other alternative d(s): 222 WARNING @ Tue, 02 Aug 2022 11:06:54: #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 11:06:54: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:06:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:06:56: 30000000 INFO @ Tue, 02 Aug 2022 11:07:03: 31000000 INFO @ Tue, 02 Aug 2022 11:07:10: 32000000 INFO @ Tue, 02 Aug 2022 11:07:14: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:07:16: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 11:07:16: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 11:07:16: #1 total tags in treatment: 9649005 INFO @ Tue, 02 Aug 2022 11:07:16: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:07:16: #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 11:07:16: #1 tags after filtering in treatment: 8763941 INFO @ Tue, 02 Aug 2022 11:07:16: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 02 Aug 2022 11:07:16: #1 finished! INFO @ Tue, 02 Aug 2022 11:07:16: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:07:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:07:17: #2 number of paired peaks: 568 WARNING @ Tue, 02 Aug 2022 11:07:17: Fewer paired peaks (568) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 568 pairs to build model! INFO @ Tue, 02 Aug 2022 11:07:17: start model_add_line... INFO @ Tue, 02 Aug 2022 11:07:17: start X-correlation... INFO @ Tue, 02 Aug 2022 11:07:17: end of X-cor INFO @ Tue, 02 Aug 2022 11:07:17: #2 finished! INFO @ Tue, 02 Aug 2022 11:07:17: #2 predicted fragment length is 222 bps INFO @ Tue, 02 Aug 2022 11:07:17: #2 alternative fragment length(s) may be 222 bps INFO @ Tue, 02 Aug 2022 11:07:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13336899/SRX13336899.20_model.r WARNING @ Tue, 02 Aug 2022 11:07:17: #2 Since the d (222) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:07:17: #2 You may need to consider one of the other alternative d(s): 222 WARNING @ Tue, 02 Aug 2022 11:07:17: #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 11:07:17: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:07:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:07:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13336899/SRX13336899.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:07:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13336899/SRX13336899.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:07:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13336899/SRX13336899.10_summits.bed INFO @ Tue, 02 Aug 2022 11:07:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (392 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:07:36: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:07:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13336899/SRX13336899.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:07:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13336899/SRX13336899.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:07:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13336899/SRX13336899.20_summits.bed INFO @ Tue, 02 Aug 2022 11:07:45: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (286 records, 4 fields): 29 millis CompletedMACS2peakCalling