[2024-01-24 13:32:34,334] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:34,336] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:34,336] [INFO] DQC Reference Directory: /var/lib/cwl/stg51a0ea84-6247-4cbb-800c-a81eb2ee27f1/dqc_reference
[2024-01-24 13:32:35,841] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:35,842] [INFO] Task started: Prodigal
[2024-01-24 13:32:35,842] [INFO] Running command: gunzip -c /var/lib/cwl/stgcd895109-2a09-455f-8d02-763df69af5e5/GCF_009811795.1_ASM981179v1_genomic.fna.gz | prodigal -d GCF_009811795.1_ASM981179v1_genomic.fna/cds.fna -a GCF_009811795.1_ASM981179v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:50,885] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:50,885] [INFO] Task started: HMMsearch
[2024-01-24 13:32:50,885] [INFO] Running command: hmmsearch --tblout GCF_009811795.1_ASM981179v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg51a0ea84-6247-4cbb-800c-a81eb2ee27f1/dqc_reference/reference_markers.hmm GCF_009811795.1_ASM981179v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:51,254] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:51,255] [INFO] Found 6/6 markers.
[2024-01-24 13:32:51,305] [INFO] Query marker FASTA was written to GCF_009811795.1_ASM981179v1_genomic.fna/markers.fasta
[2024-01-24 13:32:51,306] [INFO] Task started: Blastn
[2024-01-24 13:32:51,306] [INFO] Running command: blastn -query GCF_009811795.1_ASM981179v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51a0ea84-6247-4cbb-800c-a81eb2ee27f1/dqc_reference/reference_markers.fasta -out GCF_009811795.1_ASM981179v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:52,003] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:52,006] [INFO] Selected 28 target genomes.
[2024-01-24 13:32:52,007] [INFO] Target genome list was writen to GCF_009811795.1_ASM981179v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:52,022] [INFO] Task started: fastANI
[2024-01-24 13:32:52,022] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd895109-2a09-455f-8d02-763df69af5e5/GCF_009811795.1_ASM981179v1_genomic.fna.gz --refList GCF_009811795.1_ASM981179v1_genomic.fna/target_genomes.txt --output GCF_009811795.1_ASM981179v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:11,789] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:11,790] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg51a0ea84-6247-4cbb-800c-a81eb2ee27f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:11,791] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg51a0ea84-6247-4cbb-800c-a81eb2ee27f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:11,816] [INFO] Found 28 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:33:11,816] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:11,817] [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
Litoreibacter roseus	strain=K6	GCA_009811795.1	2601869	2601869	type	True	100.0	1477	1477	95	conclusive
Litoreibacter ponti	strain=DSM 100977	GCA_003054285.1	1510457	1510457	type	True	77.4187	298	1477	95	below_threshold
Dinoroseobacter shibae	strain=DFL 12	GCA_000018145.1	215813	215813	type	True	77.3514	180	1477	95	below_threshold
Roseobacter cerasinus	strain=AI77	GCA_009811755.1	2602289	2602289	type	True	77.3469	161	1477	95	below_threshold
Phaeobacter marinintestinus	strain=UB-M7	GCA_007923355.1	1492905	1492905	type	True	77.2101	127	1477	95	below_threshold
Litoreibacter janthinus	strain=DSM 26921	GCA_900111945.1	670154	670154	type	True	77.1048	176	1477	95	below_threshold
Litoreibacter albidus	strain=DSM 26922	GCA_900107015.1	670155	670155	type	True	77.0766	163	1477	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	77.0442	115	1477	95	below_threshold
Marivita hallyeonensis	strain=DSM 29431	GCA_900129875.1	996342	996342	type	True	77.0113	165	1477	95	below_threshold
Roseovarius confluentis	strain=SAG6	GCA_002917925.1	1852027	1852027	type	True	77.0081	147	1477	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_016583705.1	35804	35804	type	True	77.0032	141	1477	95	below_threshold
Primorskyibacter sedentarius	strain=DSM 104836	GCA_004342065.1	745311	745311	type	True	76.9865	158	1477	95	below_threshold
Rhodovulum adriaticum	strain=DSM 2781	GCA_004345735.1	35804	35804	type	True	76.9684	139	1477	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_001633165.1	35806	35806	type	True	76.9226	137	1477	95	below_threshold
Litoreibacter ascidiaceicola	strain=DSM 100566	GCA_900129235.1	1486859	1486859	type	True	76.9175	227	1477	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_000520135.2	35806	35806	type	True	76.9077	138	1477	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	76.8755	159	1477	95	below_threshold
Maritimibacter harenae	strain=DP07	GCA_009882975.1	2606218	2606218	type	True	76.8447	120	1477	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	76.8018	71	1477	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.7689	147	1477	95	below_threshold
Thalassobius aquimarinus	strain=KMM 8518	GCA_018219815.1	2785917	2785917	type	True	76.6509	145	1477	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	76.6195	82	1477	95	below_threshold
Gemmobacter aquatilis	strain=DSM 3857	GCA_900110025.1	933059	933059	type	True	76.6012	133	1477	95	below_threshold
Marivita lacus	strain=CGMCC 1.12478	GCA_014637725.1	1323742	1323742	type	True	76.5143	161	1477	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	76.4592	125	1477	95	below_threshold
Gemmobacter caeni	strain=CGMCC 1.7745	GCA_007830625.1	589035	589035	type	True	76.2089	111	1477	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	76.1895	138	1477	95	below_threshold
Gemmobacter caeni	strain=DSM 21823	GCA_003054195.1	589035	589035	type	True	76.1609	115	1477	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:11,818] [INFO] DFAST Taxonomy check result was written to GCF_009811795.1_ASM981179v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:11,819] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:11,819] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:11,819] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg51a0ea84-6247-4cbb-800c-a81eb2ee27f1/dqc_reference/checkm_data
[2024-01-24 13:33:11,821] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:11,864] [INFO] Task started: CheckM
[2024-01-24 13:33:11,864] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009811795.1_ASM981179v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009811795.1_ASM981179v1_genomic.fna/checkm_input GCF_009811795.1_ASM981179v1_genomic.fna/checkm_result
[2024-01-24 13:33:56,654] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:56,656] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:56,678] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:56,678] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:56,679] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009811795.1_ASM981179v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:56,679] [INFO] Task started: Blastn
[2024-01-24 13:33:56,679] [INFO] Running command: blastn -query GCF_009811795.1_ASM981179v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg51a0ea84-6247-4cbb-800c-a81eb2ee27f1/dqc_reference/reference_markers_gtdb.fasta -out GCF_009811795.1_ASM981179v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:57,617] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:57,622] [INFO] Selected 25 target genomes.
[2024-01-24 13:33:57,622] [INFO] Target genome list was writen to GCF_009811795.1_ASM981179v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:57,674] [INFO] Task started: fastANI
[2024-01-24 13:33:57,674] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd895109-2a09-455f-8d02-763df69af5e5/GCF_009811795.1_ASM981179v1_genomic.fna.gz --refList GCF_009811795.1_ASM981179v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009811795.1_ASM981179v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:14,212] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:14,235] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:14,236] [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
GCF_009811795.1	s__Litoreibacter roseus	100.0	1477	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003054285.1	s__Litoreibacter ponti	77.4097	299	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007923355.1	s__Phaeobacter_A marinintestinus	77.2533	124	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196965.1	s__Actibacterium_A naphthalenivorans	77.1871	171	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium_A	95.0	98.28	97.38	0.93	0.89	4	-
GCF_900111945.1	s__Litoreibacter janthinus	77.1048	176	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107015.1	s__Litoreibacter albidus	77.0766	163	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129875.1	s__Marivita hallyeonensis	77.0113	165	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002917925.1	s__Roseovarius confluentis	76.995	145	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.93	98.93	0.93	0.93	2	-
GCF_004342065.1	s__Primorskyibacter sedentarius	76.9715	159	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Primorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345735.1	s__Rhodovulum adriaticum	76.9684	139	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900129235.1	s__Litoreibacter ascidiaceicola	76.9085	228	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litoreibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000161775.1	s__Ruegeria lacuscaerulensis	76.8842	168	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCA_001730095.1	s__Leisingera sp001730095	76.8618	119	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009882975.1	s__Maritimibacter harenae	76.8447	120	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001518015.1	s__Epibacterium horizontis	76.8327	134	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011806385.1	s__Epibacterium sp011806385	76.8263	126	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363655.1	s__Roseovarius sp009363655	76.8115	167	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.13	98.13	0.93	0.93	2	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	76.7209	139	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_018219815.1	s__Thalassobius aquimarinus	76.6365	146	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255395.1	s__AWRV01 sp017255395	76.6303	152	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__AWRV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006265095.1	s__Epibacterium sp006265095	76.6244	124	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110025.1	s__Gemmobacter aquatilis	76.6012	133	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792445.1	s__Rhodobacter_B sp017792445	76.6005	183	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108275.1	s__Jhaorihella thermophila	76.4841	123	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jhaorihella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009833495.1	s__Oceanomicrobium pacificus	76.1233	122	1477	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:14,238] [INFO] GTDB search result was written to GCF_009811795.1_ASM981179v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:14,238] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:14,243] [INFO] DFAST_QC result json was written to GCF_009811795.1_ASM981179v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:14,243] [INFO] DFAST_QC completed!
[2024-01-24 13:34:14,243] [INFO] Total running time: 0h1m40s