[2023-06-30 07:54:30,372] [INFO] DFAST_QC pipeline started.
[2023-06-30 07:54:30,374] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 07:54:30,374] [INFO] DQC Reference Directory: /var/lib/cwl/stgc08e3b30-e955-4ad7-9610-e77822eef0a8/dqc_reference
[2023-06-30 07:54:31,640] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 07:54:31,641] [INFO] Task started: Prodigal
[2023-06-30 07:54:31,642] [INFO] Running command: gunzip -c /var/lib/cwl/stg104fcf5e-9b25-437c-b97b-c7ae16b7defe/GCA_903902845.1_freshwater_MAG_---_E14_bin-1579_genomic.fna.gz | prodigal -d GCA_903902845.1_freshwater_MAG_---_E14_bin-1579_genomic.fna/cds.fna -a GCA_903902845.1_freshwater_MAG_---_E14_bin-1579_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 07:54:46,034] [INFO] Task succeeded: Prodigal
[2023-06-30 07:54:46,035] [INFO] Task started: HMMsearch
[2023-06-30 07:54:46,035] [INFO] Running command: hmmsearch --tblout GCA_903902845.1_freshwater_MAG_---_E14_bin-1579_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc08e3b30-e955-4ad7-9610-e77822eef0a8/dqc_reference/reference_markers.hmm GCA_903902845.1_freshwater_MAG_---_E14_bin-1579_genomic.fna/protein.faa > /dev/null
[2023-06-30 07:54:46,325] [INFO] Task succeeded: HMMsearch
[2023-06-30 07:54:46,327] [INFO] Found 6/6 markers.
[2023-06-30 07:54:46,372] [INFO] Query marker FASTA was written to GCA_903902845.1_freshwater_MAG_---_E14_bin-1579_genomic.fna/markers.fasta
[2023-06-30 07:54:46,373] [INFO] Task started: Blastn
[2023-06-30 07:54:46,373] [INFO] Running command: blastn -query GCA_903902845.1_freshwater_MAG_---_E14_bin-1579_genomic.fna/markers.fasta -db /var/lib/cwl/stgc08e3b30-e955-4ad7-9610-e77822eef0a8/dqc_reference/reference_markers.fasta -out GCA_903902845.1_freshwater_MAG_---_E14_bin-1579_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 07:54:47,284] [INFO] Task succeeded: Blastn
[2023-06-30 07:54:47,289] [INFO] Selected 22 target genomes.
[2023-06-30 07:54:47,290] [INFO] Target genome list was writen to GCA_903902845.1_freshwater_MAG_---_E14_bin-1579_genomic.fna/target_genomes.txt
[2023-06-30 07:54:47,292] [INFO] Task started: fastANI
[2023-06-30 07:54:47,292] [INFO] Running command: fastANI --query /var/lib/cwl/stg104fcf5e-9b25-437c-b97b-c7ae16b7defe/GCA_903902845.1_freshwater_MAG_---_E14_bin-1579_genomic.fna.gz --refList GCA_903902845.1_freshwater_MAG_---_E14_bin-1579_genomic.fna/target_genomes.txt --output GCA_903902845.1_freshwater_MAG_---_E14_bin-1579_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 07:55:05,207] [INFO] Task succeeded: fastANI
[2023-06-30 07:55:05,207] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc08e3b30-e955-4ad7-9610-e77822eef0a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 07:55:05,208] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc08e3b30-e955-4ad7-9610-e77822eef0a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 07:55:05,229] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 07:55:05,229] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 07:55:05,229] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	80.8302	751	1471	95	below_threshold
Rhodopila globiformis	strain=DSM 161	GCA_002937115.1	1071	1071	type	True	78.6302	553	1471	95	below_threshold
Acidisphaera rubrifaciens	strain=HS-AP3	GCA_000964365.1	50715	50715	type	True	78.3677	294	1471	95	below_threshold
Endobacter medicaginis	strain=LMG 26838	GCA_013376135.1	1181271	1181271	type	True	78.0855	206	1471	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	77.9753	425	1471	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	77.8381	455	1471	95	below_threshold
Endobacter medicaginis	strain=CECT 8088	GCA_014192375.1	1181271	1181271	type	True	77.7035	323	1471	95	below_threshold
Siccirubricoccus deserti	strain=SYSU D8009	GCA_014283215.1	2013562	2013562	type	True	77.5757	447	1471	95	below_threshold
Siccirubricoccus deserti	strain=CGMCC 1.15936	GCA_014644195.1	2013562	2013562	type	True	77.5534	447	1471	95	below_threshold
Acidiphilium multivorum	strain=AIU301	GCA_000964345.1	62140	62140	type	True	77.5314	325	1471	95	below_threshold
Acidiphilium multivorum	strain=AIU301	GCA_000202835.1	62140	62140	type	True	77.3404	378	1471	95	below_threshold
Komagataeibacter kakiaceti	strain=JCM 25156	GCA_000613305.1	943261	943261	type	True	77.271	83	1471	95	below_threshold
Roseomonas deserti	strain=M3	GCA_001982615.1	1817963	1817963	type	True	77.2365	454	1471	95	below_threshold
Roseomonas oryzicola	strain=KCTC 22478	GCA_012163135.1	535904	535904	type	True	77.2211	420	1471	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	77.1975	335	1471	95	below_threshold
Roseomonas wenyumeiae	strain=Z23	GCA_003696345.1	2478470	2478470	type	True	77.1177	404	1471	95	below_threshold
Komagataeibacter swingsii	strain=LMG 22125	GCA_003207895.1	215220	215220	type	True	77.1104	157	1471	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	77.004	327	1471	95	below_threshold
Roseococcus thiosulfatophilus	strain=RB-3	GCA_017311575.1	35813	35813	type	True	77.0023	349	1471	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	76.8033	392	1471	95	below_threshold
Komagataeibacter rhaeticus	strain=LMG 22126	GCA_003207855.1	215221	215221	type	True	76.5659	168	1471	95	below_threshold
Sphingomonas endophytica	strain=DSM 101535	GCA_014199415.1	869719	869719	type	True	75.6595	153	1471	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 07:55:05,231] [INFO] DFAST Taxonomy check result was written to GCA_903902845.1_freshwater_MAG_---_E14_bin-1579_genomic.fna/tc_result.tsv
[2023-06-30 07:55:05,232] [INFO] ===== Taxonomy check completed =====
[2023-06-30 07:55:05,232] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 07:55:05,233] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc08e3b30-e955-4ad7-9610-e77822eef0a8/dqc_reference/checkm_data
[2023-06-30 07:55:05,235] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 07:55:05,289] [INFO] Task started: CheckM
[2023-06-30 07:55:05,290] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903902845.1_freshwater_MAG_---_E14_bin-1579_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903902845.1_freshwater_MAG_---_E14_bin-1579_genomic.fna/checkm_input GCA_903902845.1_freshwater_MAG_---_E14_bin-1579_genomic.fna/checkm_result
[2023-06-30 07:55:55,909] [INFO] Task succeeded: CheckM
[2023-06-30 07:55:55,911] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 07:55:55,962] [INFO] ===== Completeness check finished =====
[2023-06-30 07:55:55,962] [INFO] ===== Start GTDB Search =====
[2023-06-30 07:55:55,962] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903902845.1_freshwater_MAG_---_E14_bin-1579_genomic.fna/markers.fasta)
[2023-06-30 07:55:55,963] [INFO] Task started: Blastn
[2023-06-30 07:55:55,963] [INFO] Running command: blastn -query GCA_903902845.1_freshwater_MAG_---_E14_bin-1579_genomic.fna/markers.fasta -db /var/lib/cwl/stgc08e3b30-e955-4ad7-9610-e77822eef0a8/dqc_reference/reference_markers_gtdb.fasta -out GCA_903902845.1_freshwater_MAG_---_E14_bin-1579_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 07:55:57,681] [INFO] Task succeeded: Blastn
[2023-06-30 07:55:57,685] [INFO] Selected 11 target genomes.
[2023-06-30 07:55:57,685] [INFO] Target genome list was writen to GCA_903902845.1_freshwater_MAG_---_E14_bin-1579_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 07:55:57,687] [INFO] Task started: fastANI
[2023-06-30 07:55:57,688] [INFO] Running command: fastANI --query /var/lib/cwl/stg104fcf5e-9b25-437c-b97b-c7ae16b7defe/GCA_903902845.1_freshwater_MAG_---_E14_bin-1579_genomic.fna.gz --refList GCA_903902845.1_freshwater_MAG_---_E14_bin-1579_genomic.fna/target_genomes_gtdb.txt --output GCA_903902845.1_freshwater_MAG_---_E14_bin-1579_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 07:56:09,598] [INFO] Task succeeded: fastANI
[2023-06-30 07:56:09,612] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 07:56:09,613] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_903907955.1	s__BOG-930 sp903907955	99.9834	1412	1471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-930	95.0	99.93	99.75	0.97	0.94	12	conclusive
GCA_903918195.1	s__BOG-930 sp903918195	85.3881	920	1471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-930	95.0	99.84	99.84	0.94	0.94	2	-
GCA_003164455.1	s__BOG-930 sp003164455	81.7448	498	1471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-930	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903839965.1	s__BOG-930 sp903839965	81.4672	520	1471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-930	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008630155.1	s__Rhodovastum atsumiense	80.8502	727	1471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodovastum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899585.1	s__70-18 sp001899585	80.2665	618	1471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__70-18	95.0	99.94	99.94	0.98	0.98	2	-
GCA_018971455.1	s__REEB85 sp018971455	79.3313	296	1471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__REEB85	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003133265.1	s__PALSA-911 sp003133265	79.1062	400	1471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__PALSA-911	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019240395.1	s__JAFAYA01 sp019240395	78.7877	424	1471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__JAFAYA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304945.1	s__69-11 sp017304945	78.6475	470	1471	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__69-11	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 07:56:09,615] [INFO] GTDB search result was written to GCA_903902845.1_freshwater_MAG_---_E14_bin-1579_genomic.fna/result_gtdb.tsv
[2023-06-30 07:56:09,615] [INFO] ===== GTDB Search completed =====
[2023-06-30 07:56:09,619] [INFO] DFAST_QC result json was written to GCA_903902845.1_freshwater_MAG_---_E14_bin-1579_genomic.fna/dqc_result.json
[2023-06-30 07:56:09,620] [INFO] DFAST_QC completed!
[2023-06-30 07:56:09,620] [INFO] Total running time: 0h1m39s