Job ID = 6627291 SRX = SRX8521354 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:52:05 prefetch.2.10.7: 1) Downloading 'SRR11978058'... 2020-07-14T01:52:05 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:52:44 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:52:44 prefetch.2.10.7: 'SRR11978058' is valid 2020-07-14T01:52:44 prefetch.2.10.7: 1) 'SRR11978058' was downloaded successfully 2020-07-14T01:52:44 prefetch.2.10.7: 'SRR11978058' has 0 unresolved dependencies Read 3338025 spots for SRR11978058/SRR11978058.sra Written 3338025 spots for SRR11978058/SRR11978058.sra 2020-07-14T01:53:09 prefetch.2.10.7: 1) Downloading 'SRR11978059'... 2020-07-14T01:53:09 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:53:42 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:53:42 prefetch.2.10.7: 'SRR11978059' is valid 2020-07-14T01:53:42 prefetch.2.10.7: 1) 'SRR11978059' was downloaded successfully 2020-07-14T01:53:42 prefetch.2.10.7: 'SRR11978059' has 0 unresolved dependencies Read 3302152 spots for SRR11978059/SRR11978059.sra Written 3302152 spots for SRR11978059/SRR11978059.sra 2020-07-14T01:54:09 prefetch.2.10.7: 1) Downloading 'SRR11978060'... 2020-07-14T01:54:09 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:54:37 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:54:37 prefetch.2.10.7: 'SRR11978060' is valid 2020-07-14T01:54:37 prefetch.2.10.7: 1) 'SRR11978060' was downloaded successfully 2020-07-14T01:54:37 prefetch.2.10.7: 'SRR11978060' has 0 unresolved dependencies Read 3420221 spots for SRR11978060/SRR11978060.sra Written 3420221 spots for SRR11978060/SRR11978060.sra 2020-07-14T01:55:03 prefetch.2.10.7: 1) Downloading 'SRR11978061'... 2020-07-14T01:55:03 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:55:38 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:55:38 prefetch.2.10.7: 'SRR11978061' is valid 2020-07-14T01:55:38 prefetch.2.10.7: 1) 'SRR11978061' was downloaded successfully 2020-07-14T01:55:38 prefetch.2.10.7: 'SRR11978061' has 0 unresolved dependencies Read 3380988 spots for SRR11978061/SRR11978061.sra Written 3380988 spots for SRR11978061/SRR11978061.sra 2020-07-14T01:56:02 prefetch.2.10.7: 1) Downloading 'SRR11978062'... 2020-07-14T01:56:02 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:56:46 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:56:46 prefetch.2.10.7: 'SRR11978062' is valid 2020-07-14T01:56:46 prefetch.2.10.7: 1) 'SRR11978062' was downloaded successfully 2020-07-14T01:56:46 prefetch.2.10.7: 'SRR11978062' has 0 unresolved dependencies Read 10125795 spots for SRR11978062/SRR11978062.sra Written 10125795 spots for SRR11978062/SRR11978062.sra 2020-07-14T01:57:34 prefetch.2.10.7: 1) Downloading 'SRR11978063'... 2020-07-14T01:57:34 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:58:46 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:58:46 prefetch.2.10.7: 'SRR11978063' is valid 2020-07-14T01:58:46 prefetch.2.10.7: 1) 'SRR11978063' was downloaded successfully 2020-07-14T01:58:46 prefetch.2.10.7: 'SRR11978063' has 0 unresolved dependencies Read 9263511 spots for SRR11978063/SRR11978063.sra Written 9263511 spots for SRR11978063/SRR11978063.sra 2020-07-14T01:59:31 prefetch.2.10.7: 1) Downloading 'SRR11978064'... 2020-07-14T01:59:31 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:01:06 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:01:06 prefetch.2.10.7: 'SRR11978064' is valid 2020-07-14T02:01:06 prefetch.2.10.7: 1) 'SRR11978064' was downloaded successfully 2020-07-14T02:01:06 prefetch.2.10.7: 'SRR11978064' has 0 unresolved dependencies Read 9641357 spots for SRR11978064/SRR11978064.sra Written 9641357 spots for SRR11978064/SRR11978064.sra 2020-07-14T02:02:18 prefetch.2.10.7: 1) Downloading 'SRR11978065'... 2020-07-14T02:02:18 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:03:24 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:03:25 prefetch.2.10.7: 'SRR11978065' is valid 2020-07-14T02:03:25 prefetch.2.10.7: 1) 'SRR11978065' was downloaded successfully 2020-07-14T02:03:25 prefetch.2.10.7: 'SRR11978065' has 0 unresolved dependencies Read 9720196 spots for SRR11978065/SRR11978065.sra Written 9720196 spots for SRR11978065/SRR11978065.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627534 ("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: 00:09:10 52192245 reads; of these: 52192245 (100.00%) were unpaired; of these: 40938687 (78.44%) aligned 0 times 8288697 (15.88%) aligned exactly 1 time 2964861 (5.68%) aligned >1 times 21.56% overall alignment rate Time searching: 00:09:10 Overall time: 00:09:10 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_sort_core] merging from 8 files... [bam_rmdupse_core] 2169656 / 11253558 = 0.1928 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 11:17:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521354/SRX8521354.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521354/SRX8521354.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521354/SRX8521354.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521354/SRX8521354.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 11:17:03: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:17:03: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:17:09: 1000000 INFO @ Tue, 14 Jul 2020 11:17:14: 2000000 INFO @ Tue, 14 Jul 2020 11:17:19: 3000000 INFO @ Tue, 14 Jul 2020 11:17:24: 4000000 INFO @ Tue, 14 Jul 2020 11:17:29: 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 11:17:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521354/SRX8521354.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521354/SRX8521354.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521354/SRX8521354.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521354/SRX8521354.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 11:17:33: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:17:33: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:17:34: 6000000 INFO @ Tue, 14 Jul 2020 11:17:39: 1000000 INFO @ Tue, 14 Jul 2020 11:17:40: 7000000 INFO @ Tue, 14 Jul 2020 11:17:44: 2000000 INFO @ Tue, 14 Jul 2020 11:17:45: 8000000 INFO @ Tue, 14 Jul 2020 11:17:49: 3000000 INFO @ Tue, 14 Jul 2020 11:17:50: 9000000 INFO @ Tue, 14 Jul 2020 11:17:51: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 11:17:51: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 11:17:51: #1 total tags in treatment: 9083902 INFO @ Tue, 14 Jul 2020 11:17:51: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:17:51: #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 11:17:51: #1 tags after filtering in treatment: 9083902 INFO @ Tue, 14 Jul 2020 11:17:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:17:51: #1 finished! INFO @ Tue, 14 Jul 2020 11:17:51: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:17:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:17:51: #2 number of paired peaks: 182 WARNING @ Tue, 14 Jul 2020 11:17:51: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Tue, 14 Jul 2020 11:17:51: start model_add_line... INFO @ Tue, 14 Jul 2020 11:17:52: start X-correlation... INFO @ Tue, 14 Jul 2020 11:17:52: end of X-cor INFO @ Tue, 14 Jul 2020 11:17:52: #2 finished! INFO @ Tue, 14 Jul 2020 11:17:52: #2 predicted fragment length is 53 bps INFO @ Tue, 14 Jul 2020 11:17:52: #2 alternative fragment length(s) may be 53 bps INFO @ Tue, 14 Jul 2020 11:17:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521354/SRX8521354.05_model.r WARNING @ Tue, 14 Jul 2020 11:17:52: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:17:52: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Tue, 14 Jul 2020 11:17:52: #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 11:17:52: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:17:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:17:55: 4000000 INFO @ Tue, 14 Jul 2020 11:18:00: 5000000 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 11:18:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521354/SRX8521354.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521354/SRX8521354.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521354/SRX8521354.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521354/SRX8521354.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 11:18:03: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:18:03: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:18:05: 6000000 INFO @ Tue, 14 Jul 2020 11:18:09: 1000000 INFO @ Tue, 14 Jul 2020 11:18:09: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:18:10: 7000000 INFO @ Tue, 14 Jul 2020 11:18:15: 2000000 INFO @ Tue, 14 Jul 2020 11:18:16: 8000000 INFO @ Tue, 14 Jul 2020 11:18:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521354/SRX8521354.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:18:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521354/SRX8521354.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:18:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521354/SRX8521354.05_summits.bed INFO @ Tue, 14 Jul 2020 11:18:19: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2196 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:18:21: 9000000 INFO @ Tue, 14 Jul 2020 11:18:22: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 11:18:22: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 11:18:22: #1 total tags in treatment: 9083902 INFO @ Tue, 14 Jul 2020 11:18:22: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:18:22: #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 11:18:22: 3000000 INFO @ Tue, 14 Jul 2020 11:18:22: #1 tags after filtering in treatment: 9083902 INFO @ Tue, 14 Jul 2020 11:18:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:18:22: #1 finished! INFO @ Tue, 14 Jul 2020 11:18:22: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:18:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:18:22: #2 number of paired peaks: 182 WARNING @ Tue, 14 Jul 2020 11:18:22: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Tue, 14 Jul 2020 11:18:22: start model_add_line... INFO @ Tue, 14 Jul 2020 11:18:22: start X-correlation... INFO @ Tue, 14 Jul 2020 11:18:22: end of X-cor INFO @ Tue, 14 Jul 2020 11:18:22: #2 finished! INFO @ Tue, 14 Jul 2020 11:18:22: #2 predicted fragment length is 53 bps INFO @ Tue, 14 Jul 2020 11:18:22: #2 alternative fragment length(s) may be 53 bps INFO @ Tue, 14 Jul 2020 11:18:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521354/SRX8521354.10_model.r WARNING @ Tue, 14 Jul 2020 11:18:22: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:18:22: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Tue, 14 Jul 2020 11:18:22: #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 11:18:22: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:18:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:18:27: 4000000 INFO @ Tue, 14 Jul 2020 11:18:33: 5000000 INFO @ Tue, 14 Jul 2020 11:18:38: 6000000 INFO @ Tue, 14 Jul 2020 11:18:41: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:18:43: 7000000 INFO @ Tue, 14 Jul 2020 11:18:49: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:18:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521354/SRX8521354.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:18:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521354/SRX8521354.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:18:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521354/SRX8521354.10_summits.bed INFO @ Tue, 14 Jul 2020 11:18:50: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (963 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:18:54: 9000000 INFO @ Tue, 14 Jul 2020 11:18:54: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 11:18:54: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 11:18:54: #1 total tags in treatment: 9083902 INFO @ Tue, 14 Jul 2020 11:18:54: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:18:54: #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 11:18:55: #1 tags after filtering in treatment: 9083902 INFO @ Tue, 14 Jul 2020 11:18:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:18:55: #1 finished! INFO @ Tue, 14 Jul 2020 11:18:55: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:18:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:18:55: #2 number of paired peaks: 182 WARNING @ Tue, 14 Jul 2020 11:18:55: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Tue, 14 Jul 2020 11:18:55: start model_add_line... INFO @ Tue, 14 Jul 2020 11:18:55: start X-correlation... INFO @ Tue, 14 Jul 2020 11:18:55: end of X-cor INFO @ Tue, 14 Jul 2020 11:18:55: #2 finished! INFO @ Tue, 14 Jul 2020 11:18:55: #2 predicted fragment length is 53 bps INFO @ Tue, 14 Jul 2020 11:18:55: #2 alternative fragment length(s) may be 53 bps INFO @ Tue, 14 Jul 2020 11:18:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521354/SRX8521354.20_model.r WARNING @ Tue, 14 Jul 2020 11:18:55: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:18:55: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Tue, 14 Jul 2020 11:18:55: #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 11:18:55: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:18:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:19:13: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:19:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521354/SRX8521354.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:19:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521354/SRX8521354.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:19:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521354/SRX8521354.20_summits.bed INFO @ Tue, 14 Jul 2020 11:19:23: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (183 records, 4 fields): 2 millis CompletedMACS2peakCalling