Job ID = 16435590 SRX = SRX13110373 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T01:50:57 prefetch.2.10.7: 1) Downloading 'SRR16918043'... 2022-08-02T01:50:57 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T01:51:35 prefetch.2.10.7: HTTPS download succeed 2022-08-02T01:51:35 prefetch.2.10.7: 1) 'SRR16918043' was downloaded successfully 2022-08-02T01:51:35 prefetch.2.10.7: 'SRR16918043' has 0 unresolved dependencies Read 21108072 spots for SRR16918043/SRR16918043.sra Written 21108072 spots for SRR16918043/SRR16918043.sra fastq に変換しました。 bowtie でマッピング中... Your job 16436170 ("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: 00:06:32 21108072 reads; of these: 21108072 (100.00%) were unpaired; of these: 2450095 (11.61%) aligned 0 times 15752752 (74.63%) aligned exactly 1 time 2905225 (13.76%) aligned >1 times 88.39% overall alignment rate Time searching: 00:06:32 Overall time: 00:06:32 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 8 files... [bam_rmdupse_core] 2174655 / 18657977 = 0.1166 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 11:03:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110373/SRX13110373.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110373/SRX13110373.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110373/SRX13110373.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110373/SRX13110373.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 11:03:59: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:03:59: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:04:06: 1000000 INFO @ Tue, 02 Aug 2022 11:04:13: 2000000 INFO @ Tue, 02 Aug 2022 11:04:20: 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 11:04:26: 4000000 INFO @ Tue, 02 Aug 2022 11:04:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110373/SRX13110373.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110373/SRX13110373.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110373/SRX13110373.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110373/SRX13110373.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 11:04:28: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:04:28: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:04:34: 5000000 INFO @ Tue, 02 Aug 2022 11:04:35: 1000000 INFO @ Tue, 02 Aug 2022 11:04:41: 2000000 INFO @ Tue, 02 Aug 2022 11:04:41: 6000000 INFO @ Tue, 02 Aug 2022 11:04:48: 3000000 INFO @ Tue, 02 Aug 2022 11:04:49: 7000000 INFO @ Tue, 02 Aug 2022 11:04:55: 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 11:04:57: 8000000 INFO @ Tue, 02 Aug 2022 11:04:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX13110373/SRX13110373.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX13110373/SRX13110373.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX13110373/SRX13110373.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX13110373/SRX13110373.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 11:04:58: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:04:58: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:05:02: 5000000 INFO @ Tue, 02 Aug 2022 11:05:04: 9000000 INFO @ Tue, 02 Aug 2022 11:05:05: 1000000 INFO @ Tue, 02 Aug 2022 11:05:08: 6000000 INFO @ Tue, 02 Aug 2022 11:05:12: 10000000 INFO @ Tue, 02 Aug 2022 11:05:12: 2000000 INFO @ Tue, 02 Aug 2022 11:05:15: 7000000 INFO @ Tue, 02 Aug 2022 11:05:19: 11000000 INFO @ Tue, 02 Aug 2022 11:05:20: 3000000 INFO @ Tue, 02 Aug 2022 11:05:22: 8000000 INFO @ Tue, 02 Aug 2022 11:05:27: 4000000 INFO @ Tue, 02 Aug 2022 11:05:27: 12000000 INFO @ Tue, 02 Aug 2022 11:05:29: 9000000 INFO @ Tue, 02 Aug 2022 11:05:34: 5000000 INFO @ Tue, 02 Aug 2022 11:05:35: 13000000 INFO @ Tue, 02 Aug 2022 11:05:36: 10000000 INFO @ Tue, 02 Aug 2022 11:05:41: 6000000 INFO @ Tue, 02 Aug 2022 11:05:42: 11000000 INFO @ Tue, 02 Aug 2022 11:05:42: 14000000 INFO @ Tue, 02 Aug 2022 11:05:49: 7000000 INFO @ Tue, 02 Aug 2022 11:05:49: 12000000 INFO @ Tue, 02 Aug 2022 11:05:50: 15000000 INFO @ Tue, 02 Aug 2022 11:05:56: 8000000 INFO @ Tue, 02 Aug 2022 11:05:56: 13000000 INFO @ Tue, 02 Aug 2022 11:05:57: 16000000 INFO @ Tue, 02 Aug 2022 11:06:01: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:06:01: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:06:01: #1 total tags in treatment: 16483322 INFO @ Tue, 02 Aug 2022 11:06:01: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:06:01: #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 11:06:01: #1 tags after filtering in treatment: 16483322 INFO @ Tue, 02 Aug 2022 11:06:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:06:01: #1 finished! INFO @ Tue, 02 Aug 2022 11:06:01: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:06:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:06:02: #2 number of paired peaks: 213 WARNING @ Tue, 02 Aug 2022 11:06:02: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Tue, 02 Aug 2022 11:06:02: start model_add_line... INFO @ Tue, 02 Aug 2022 11:06:02: start X-correlation... INFO @ Tue, 02 Aug 2022 11:06:02: end of X-cor INFO @ Tue, 02 Aug 2022 11:06:02: #2 finished! INFO @ Tue, 02 Aug 2022 11:06:02: #2 predicted fragment length is 73 bps INFO @ Tue, 02 Aug 2022 11:06:02: #2 alternative fragment length(s) may be 2,73 bps INFO @ Tue, 02 Aug 2022 11:06:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110373/SRX13110373.05_model.r WARNING @ Tue, 02 Aug 2022 11:06:02: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:06:02: #2 You may need to consider one of the other alternative d(s): 2,73 WARNING @ Tue, 02 Aug 2022 11:06:02: #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 11:06:02: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:06:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:06:03: 14000000 INFO @ Tue, 02 Aug 2022 11:06:03: 9000000 INFO @ Tue, 02 Aug 2022 11:06:09: 15000000 INFO @ Tue, 02 Aug 2022 11:06:11: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:06:16: 16000000 INFO @ Tue, 02 Aug 2022 11:06:18: 11000000 INFO @ Tue, 02 Aug 2022 11:06:19: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:06:19: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:06:19: #1 total tags in treatment: 16483322 INFO @ Tue, 02 Aug 2022 11:06:19: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:06:19: #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 11:06:19: #1 tags after filtering in treatment: 16483322 INFO @ Tue, 02 Aug 2022 11:06:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:06:19: #1 finished! INFO @ Tue, 02 Aug 2022 11:06:19: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:06:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:06:21: #2 number of paired peaks: 213 WARNING @ Tue, 02 Aug 2022 11:06:21: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Tue, 02 Aug 2022 11:06:21: start model_add_line... INFO @ Tue, 02 Aug 2022 11:06:21: start X-correlation... INFO @ Tue, 02 Aug 2022 11:06:21: end of X-cor INFO @ Tue, 02 Aug 2022 11:06:21: #2 finished! INFO @ Tue, 02 Aug 2022 11:06:21: #2 predicted fragment length is 73 bps INFO @ Tue, 02 Aug 2022 11:06:21: #2 alternative fragment length(s) may be 2,73 bps INFO @ Tue, 02 Aug 2022 11:06:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110373/SRX13110373.10_model.r WARNING @ Tue, 02 Aug 2022 11:06:21: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:06:21: #2 You may need to consider one of the other alternative d(s): 2,73 WARNING @ Tue, 02 Aug 2022 11:06:21: #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 11:06:21: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:06:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:06:25: 12000000 INFO @ Tue, 02 Aug 2022 11:06:31: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:06:32: 13000000 INFO @ Tue, 02 Aug 2022 11:06:39: 14000000 INFO @ Tue, 02 Aug 2022 11:06:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110373/SRX13110373.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:06:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110373/SRX13110373.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:06:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110373/SRX13110373.05_summits.bed INFO @ Tue, 02 Aug 2022 11:06:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (721 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:06:45: 15000000 INFO @ Tue, 02 Aug 2022 11:06:49: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:06:52: 16000000 INFO @ Tue, 02 Aug 2022 11:06:55: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:06:55: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:06:55: #1 total tags in treatment: 16483322 INFO @ Tue, 02 Aug 2022 11:06:55: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:06:55: #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 11:06:56: #1 tags after filtering in treatment: 16483322 INFO @ Tue, 02 Aug 2022 11:06:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:06:56: #1 finished! INFO @ Tue, 02 Aug 2022 11:06:56: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:06:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:06:57: #2 number of paired peaks: 213 WARNING @ Tue, 02 Aug 2022 11:06:57: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Tue, 02 Aug 2022 11:06:57: start model_add_line... INFO @ Tue, 02 Aug 2022 11:06:57: start X-correlation... INFO @ Tue, 02 Aug 2022 11:06:57: end of X-cor INFO @ Tue, 02 Aug 2022 11:06:57: #2 finished! INFO @ Tue, 02 Aug 2022 11:06:57: #2 predicted fragment length is 73 bps INFO @ Tue, 02 Aug 2022 11:06:57: #2 alternative fragment length(s) may be 2,73 bps INFO @ Tue, 02 Aug 2022 11:06:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX13110373/SRX13110373.20_model.r WARNING @ Tue, 02 Aug 2022 11:06:57: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:06:57: #2 You may need to consider one of the other alternative d(s): 2,73 WARNING @ Tue, 02 Aug 2022 11:06:57: #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 11:06:57: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:06:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:07:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110373/SRX13110373.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:07:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110373/SRX13110373.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:07:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110373/SRX13110373.10_summits.bed INFO @ Tue, 02 Aug 2022 11:07:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (437 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:07:25: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:07:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX13110373/SRX13110373.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:07:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX13110373/SRX13110373.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:07:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX13110373/SRX13110373.20_summits.bed INFO @ Tue, 02 Aug 2022 11:07:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (231 records, 4 fields): 55 millis CompletedMACS2peakCalling