Job ID = 6627163 SRX = SRX8521301 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:23:06 prefetch.2.10.7: 1) Downloading 'SRR11978526'... 2020-07-14T01:23:06 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:24:26 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:24:26 prefetch.2.10.7: 'SRR11978526' is valid 2020-07-14T01:24:26 prefetch.2.10.7: 1) 'SRR11978526' was downloaded successfully 2020-07-14T01:24:26 prefetch.2.10.7: 'SRR11978526' has 0 unresolved dependencies Read 11027297 spots for SRR11978526/SRR11978526.sra Written 11027297 spots for SRR11978526/SRR11978526.sra 2020-07-14T01:25:13 prefetch.2.10.7: 1) Downloading 'SRR11978527'... 2020-07-14T01:25:13 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:26:31 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:26:32 prefetch.2.10.7: 'SRR11978527' is valid 2020-07-14T01:26:32 prefetch.2.10.7: 1) 'SRR11978527' was downloaded successfully 2020-07-14T01:26:32 prefetch.2.10.7: 'SRR11978527' has 0 unresolved dependencies Read 10878682 spots for SRR11978527/SRR11978527.sra Written 10878682 spots for SRR11978527/SRR11978527.sra 2020-07-14T01:27:22 prefetch.2.10.7: 1) Downloading 'SRR11978528'... 2020-07-14T01:27:22 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:28:36 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:28:37 prefetch.2.10.7: 'SRR11978528' is valid 2020-07-14T01:28:37 prefetch.2.10.7: 1) 'SRR11978528' was downloaded successfully 2020-07-14T01:28:37 prefetch.2.10.7: 'SRR11978528' has 0 unresolved dependencies Read 11153572 spots for SRR11978528/SRR11978528.sra Written 11153572 spots for SRR11978528/SRR11978528.sra 2020-07-14T01:29:27 prefetch.2.10.7: 1) Downloading 'SRR11978529'... 2020-07-14T01:29:27 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:31:01 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:31:02 prefetch.2.10.7: 'SRR11978529' is valid 2020-07-14T01:31:02 prefetch.2.10.7: 1) 'SRR11978529' was downloaded successfully 2020-07-14T01:31:02 prefetch.2.10.7: 'SRR11978529' has 0 unresolved dependencies Read 10907285 spots for SRR11978529/SRR11978529.sra Written 10907285 spots for SRR11978529/SRR11978529.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627424 ("srTdm6") 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: 00:09:09 43966836 reads; of these: 43966836 (100.00%) were unpaired; of these: 35031652 (79.68%) aligned 0 times 6008724 (13.67%) aligned exactly 1 time 2926460 (6.66%) aligned >1 times 20.32% overall alignment rate Time searching: 00:09:09 Overall time: 00:09:09 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 1889798 / 8935184 = 0.2115 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 10:43:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521301/SRX8521301.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521301/SRX8521301.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521301/SRX8521301.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521301/SRX8521301.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 14 Jul 2020 10:43:56: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:43:56: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:44:02: 1000000 INFO @ Tue, 14 Jul 2020 10:44:07: 2000000 INFO @ Tue, 14 Jul 2020 10:44:13: 3000000 INFO @ Tue, 14 Jul 2020 10:44:18: 4000000 INFO @ Tue, 14 Jul 2020 10:44:24: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 10:44:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521301/SRX8521301.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521301/SRX8521301.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521301/SRX8521301.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521301/SRX8521301.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 14 Jul 2020 10:44:26: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:44:26: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:44:30: 6000000 INFO @ Tue, 14 Jul 2020 10:44:34: 1000000 INFO @ Tue, 14 Jul 2020 10:44:35: 7000000 INFO @ Tue, 14 Jul 2020 10:44:36: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 10:44:36: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 10:44:36: #1 total tags in treatment: 7045386 INFO @ Tue, 14 Jul 2020 10:44:36: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:44:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:44:36: #1 tags after filtering in treatment: 7045386 INFO @ Tue, 14 Jul 2020 10:44:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:44:36: #1 finished! INFO @ Tue, 14 Jul 2020 10:44:36: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:44:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:44:36: #2 number of paired peaks: 204 WARNING @ Tue, 14 Jul 2020 10:44:36: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Tue, 14 Jul 2020 10:44:36: start model_add_line... INFO @ Tue, 14 Jul 2020 10:44:36: start X-correlation... INFO @ Tue, 14 Jul 2020 10:44:36: end of X-cor INFO @ Tue, 14 Jul 2020 10:44:36: #2 finished! INFO @ Tue, 14 Jul 2020 10:44:36: #2 predicted fragment length is 61 bps INFO @ Tue, 14 Jul 2020 10:44:36: #2 alternative fragment length(s) may be 61,532 bps INFO @ Tue, 14 Jul 2020 10:44:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521301/SRX8521301.05_model.r WARNING @ Tue, 14 Jul 2020 10:44:36: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:44:36: #2 You may need to consider one of the other alternative d(s): 61,532 WARNING @ Tue, 14 Jul 2020 10:44:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:44:36: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:44:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:44:43: 2000000 INFO @ Tue, 14 Jul 2020 10:44:50: 3000000 INFO @ Tue, 14 Jul 2020 10:44:51: #3 Call peaks for each chromosome... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 10:44:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521301/SRX8521301.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521301/SRX8521301.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521301/SRX8521301.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521301/SRX8521301.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 14 Jul 2020 10:44:56: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:44:56: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:44:57: 4000000 INFO @ Tue, 14 Jul 2020 10:44:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521301/SRX8521301.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:44:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521301/SRX8521301.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:44:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521301/SRX8521301.05_summits.bed INFO @ Tue, 14 Jul 2020 10:44:58: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1854 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:45:02: 1000000 INFO @ Tue, 14 Jul 2020 10:45:03: 5000000 INFO @ Tue, 14 Jul 2020 10:45:07: 2000000 INFO @ Tue, 14 Jul 2020 10:45:10: 6000000 INFO @ Tue, 14 Jul 2020 10:45:13: 3000000 INFO @ Tue, 14 Jul 2020 10:45:17: 7000000 INFO @ Tue, 14 Jul 2020 10:45:17: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 10:45:17: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 10:45:17: #1 total tags in treatment: 7045386 INFO @ Tue, 14 Jul 2020 10:45:17: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:45:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:45:17: #1 tags after filtering in treatment: 7045386 INFO @ Tue, 14 Jul 2020 10:45:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:45:17: #1 finished! INFO @ Tue, 14 Jul 2020 10:45:17: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:45:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:45:18: #2 number of paired peaks: 204 WARNING @ Tue, 14 Jul 2020 10:45:18: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Tue, 14 Jul 2020 10:45:18: start model_add_line... INFO @ Tue, 14 Jul 2020 10:45:18: start X-correlation... INFO @ Tue, 14 Jul 2020 10:45:18: end of X-cor INFO @ Tue, 14 Jul 2020 10:45:18: #2 finished! INFO @ Tue, 14 Jul 2020 10:45:18: #2 predicted fragment length is 61 bps INFO @ Tue, 14 Jul 2020 10:45:18: #2 alternative fragment length(s) may be 61,532 bps INFO @ Tue, 14 Jul 2020 10:45:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521301/SRX8521301.10_model.r WARNING @ Tue, 14 Jul 2020 10:45:18: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:45:18: #2 You may need to consider one of the other alternative d(s): 61,532 WARNING @ Tue, 14 Jul 2020 10:45:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:45:18: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:45:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:45:19: 4000000 INFO @ Tue, 14 Jul 2020 10:45:25: 5000000 INFO @ Tue, 14 Jul 2020 10:45:30: 6000000 INFO @ Tue, 14 Jul 2020 10:45:32: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:45:36: 7000000 INFO @ Tue, 14 Jul 2020 10:45:36: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 10:45:36: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 10:45:36: #1 total tags in treatment: 7045386 INFO @ Tue, 14 Jul 2020 10:45:36: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:45:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:45:36: #1 tags after filtering in treatment: 7045386 INFO @ Tue, 14 Jul 2020 10:45:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:45:36: #1 finished! INFO @ Tue, 14 Jul 2020 10:45:36: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:45:36: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:45:37: #2 number of paired peaks: 204 WARNING @ Tue, 14 Jul 2020 10:45:37: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Tue, 14 Jul 2020 10:45:37: start model_add_line... INFO @ Tue, 14 Jul 2020 10:45:37: start X-correlation... INFO @ Tue, 14 Jul 2020 10:45:37: end of X-cor INFO @ Tue, 14 Jul 2020 10:45:37: #2 finished! INFO @ Tue, 14 Jul 2020 10:45:37: #2 predicted fragment length is 61 bps INFO @ Tue, 14 Jul 2020 10:45:37: #2 alternative fragment length(s) may be 61,532 bps INFO @ Tue, 14 Jul 2020 10:45:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521301/SRX8521301.20_model.r WARNING @ Tue, 14 Jul 2020 10:45:37: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:45:37: #2 You may need to consider one of the other alternative d(s): 61,532 WARNING @ Tue, 14 Jul 2020 10:45:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:45:37: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:45:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:45:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521301/SRX8521301.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:45:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521301/SRX8521301.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:45:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521301/SRX8521301.10_summits.bed INFO @ Tue, 14 Jul 2020 10:45:39: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (891 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:45:51: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:45:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521301/SRX8521301.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:45:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521301/SRX8521301.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:45:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521301/SRX8521301.20_summits.bed INFO @ Tue, 14 Jul 2020 10:45:59: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (264 records, 4 fields): 1 millis CompletedMACS2peakCalling