[2024-01-24 13:49:32,697] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:32,699] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:32,704] [INFO] DQC Reference Directory: /var/lib/cwl/stg92cfd3f8-cdb6-453f-8317-1ee5d5fee16e/dqc_reference
[2024-01-24 13:49:34,090] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:34,091] [INFO] Task started: Prodigal
[2024-01-24 13:49:34,092] [INFO] Running command: gunzip -c /var/lib/cwl/stg88f736db-ad83-4cc6-b0d2-a2fb7146a0f1/GCF_019061145.1_ASM1906114v1_genomic.fna.gz | prodigal -d GCF_019061145.1_ASM1906114v1_genomic.fna/cds.fna -a GCF_019061145.1_ASM1906114v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:45,951] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:45,951] [INFO] Task started: HMMsearch
[2024-01-24 13:49:45,952] [INFO] Running command: hmmsearch --tblout GCF_019061145.1_ASM1906114v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg92cfd3f8-cdb6-453f-8317-1ee5d5fee16e/dqc_reference/reference_markers.hmm GCF_019061145.1_ASM1906114v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:46,253] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:46,255] [INFO] Found 6/6 markers.
[2024-01-24 13:49:46,288] [INFO] Query marker FASTA was written to GCF_019061145.1_ASM1906114v1_genomic.fna/markers.fasta
[2024-01-24 13:49:46,288] [INFO] Task started: Blastn
[2024-01-24 13:49:46,288] [INFO] Running command: blastn -query GCF_019061145.1_ASM1906114v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92cfd3f8-cdb6-453f-8317-1ee5d5fee16e/dqc_reference/reference_markers.fasta -out GCF_019061145.1_ASM1906114v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:47,336] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:47,339] [INFO] Selected 29 target genomes.
[2024-01-24 13:49:47,339] [INFO] Target genome list was writen to GCF_019061145.1_ASM1906114v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:47,348] [INFO] Task started: fastANI
[2024-01-24 13:49:47,348] [INFO] Running command: fastANI --query /var/lib/cwl/stg88f736db-ad83-4cc6-b0d2-a2fb7146a0f1/GCF_019061145.1_ASM1906114v1_genomic.fna.gz --refList GCF_019061145.1_ASM1906114v1_genomic.fna/target_genomes.txt --output GCF_019061145.1_ASM1906114v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:08,519] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:08,519] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg92cfd3f8-cdb6-453f-8317-1ee5d5fee16e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:08,519] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg92cfd3f8-cdb6-453f-8317-1ee5d5fee16e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:08,541] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:50:08,541] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:50:08,542] [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
Rhodovulum marinum	strain=DSM 18063	GCA_004343075.1	320662	320662	type	True	79.1997	510	1206	95	below_threshold
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	79.0692	354	1206	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	79.0045	486	1206	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	78.9597	494	1206	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	78.8606	487	1206	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	78.8558	415	1206	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	78.6869	456	1206	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	78.6706	514	1206	95	below_threshold
Rhodovulum visakhapatnamense	strain=JA181	GCA_004365965.1	364297	364297	type	True	78.6285	501	1206	95	below_threshold
Mameliella alba	strain=CGMCC 1.7290	GCA_900101505.1	561184	561184	suspected-type	True	78.593	509	1206	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_000520135.2	35806	35806	type	True	78.5688	466	1206	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	78.5683	515	1206	95	below_threshold
Maritimibacter harenae	strain=DP07	GCA_009882975.1	2606218	2606218	type	True	78.5313	483	1206	95	below_threshold
Rhodovulum sulfidophilum	strain=DSM 1374	GCA_001633165.1	35806	35806	type	True	78.5288	471	1206	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.5096	519	1206	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	78.5003	407	1206	95	below_threshold
Wenxinia saemankumensis	strain=DSM 100565	GCA_900141735.1	1447782	1447782	type	True	78.4608	442	1206	95	below_threshold
Kangsaoukella pontilimi	strain=GH1-50	GCA_009830125.1	2691042	2691042	type	True	78.4298	418	1206	95	below_threshold
Pseudoroseicyclus aestuarii	strain=CECT 9025	GCA_003217255.1	1795041	1795041	type	True	78.3714	405	1206	95	below_threshold
Silicimonas algicola	strain=KC90	GCA_003970735.1	1826607	1826607	type	True	78.3317	413	1206	95	below_threshold
Salipiger aestuarii	strain=AD8	GCA_008930655.1	568098	568098	type	True	78.3204	387	1206	95	below_threshold
Silicimonas algicola	strain=DSM 103371	GCA_003148765.1	1826607	1826607	type	True	78.2911	415	1206	95	below_threshold
Thioclava sediminum	strain=TAW-CT134	GCA_002020355.1	1915319	1915319	type	True	78.2272	387	1206	95	below_threshold
Salipiger aestuarii	strain=DSM 22011	GCA_003259905.1	568098	568098	type	True	78.2195	394	1206	95	below_threshold
Thioclava atlantica	strain=13D2W-2	GCA_000737065.1	1317124	1317124	type	True	78.217	395	1206	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	78.1899	416	1206	95	below_threshold
Mangrovicoccus ximenensis	strain=T1lg56	GCA_003056725.1	1911570	1911570	type	True	78.0584	410	1206	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.9482	399	1206	95	below_threshold
Actibacterium lipolyticum	strain=CECT 8621	GCA_900184935.1	1524263	1524263	type	True	77.0026	241	1206	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:08,543] [INFO] DFAST Taxonomy check result was written to GCF_019061145.1_ASM1906114v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:08,544] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:08,544] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:08,544] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg92cfd3f8-cdb6-453f-8317-1ee5d5fee16e/dqc_reference/checkm_data
[2024-01-24 13:50:08,545] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:08,604] [INFO] Task started: CheckM
[2024-01-24 13:50:08,604] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019061145.1_ASM1906114v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019061145.1_ASM1906114v1_genomic.fna/checkm_input GCF_019061145.1_ASM1906114v1_genomic.fna/checkm_result
[2024-01-24 13:50:48,132] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:48,133] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:48,152] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:48,152] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:48,153] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019061145.1_ASM1906114v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:48,153] [INFO] Task started: Blastn
[2024-01-24 13:50:48,153] [INFO] Running command: blastn -query GCF_019061145.1_ASM1906114v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92cfd3f8-cdb6-453f-8317-1ee5d5fee16e/dqc_reference/reference_markers_gtdb.fasta -out GCF_019061145.1_ASM1906114v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:49,999] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:50,003] [INFO] Selected 27 target genomes.
[2024-01-24 13:50:50,003] [INFO] Target genome list was writen to GCF_019061145.1_ASM1906114v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:50,019] [INFO] Task started: fastANI
[2024-01-24 13:50:50,019] [INFO] Running command: fastANI --query /var/lib/cwl/stg88f736db-ad83-4cc6-b0d2-a2fb7146a0f1/GCF_019061145.1_ASM1906114v1_genomic.fna.gz --refList GCF_019061145.1_ASM1906114v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019061145.1_ASM1906114v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:11,681] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:11,708] [INFO] Found 27 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:11,708] [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_019061145.1	s__ASV31 sp019061145	100.0	1205	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ASV31	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002701395.1	s__Rhodobacter_B sp002701395	79.3389	595	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017792445.1	s__Rhodobacter_B sp017792445	79.2434	604	1206	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_018139985.1	s__JAGSOU01 sp018139985	79.2356	530	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004343075.1	s__Rhodovulum marinum	79.1872	511	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107235.1	s__Citreimonas salinaria	79.1795	501	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Citreimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003344785.1	s__Puniceibacterium profundi	79.0945	572	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002869745.1	s__Oceaniglobus roseus	78.9932	581	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339675.1	s__Rhodovulum steppense	78.9599	494	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	78.9362	505	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002797755.1	s__Brevirhabdus pacifica	78.8575	416	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Brevirhabdus	95.0	99.99	99.97	0.99	0.98	4	-
GCF_009649175.1	s__Rhodovulum strictum	78.814	492	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003053725.1	s__Rhodovulum kholense	78.7999	502	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	98.27	98.27	0.96	0.96	2	-
GCF_900172355.1	s__Oceanicola antarcticus	78.6871	492	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	78.6528	491	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017311415.1	s__Salipiger abyssi_A	78.6243	474	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379485.1	s__Wenxinia marina	78.5798	497	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	99.99	99.99	0.99	0.99	3	-
GCF_900101505.1	s__Mameliella alba	78.5764	511	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mameliella	95.0	98.60	98.14	0.96	0.94	14	-
GCF_005938215.1	s__Ruegeria sediminis	78.5445	444	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009882975.1	s__Maritimibacter harenae	78.5223	484	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Maritimibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009830125.1	s__GH1-50 sp009830125	78.4203	419	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__GH1-50	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000169415.1	s__Sagittula stellata	78.4148	453	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217255.1	s__Pseudoroseicyclus aestuarii	78.3862	404	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoroseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008710275.1	s__Oceanicola sp008710275	78.3195	435	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259905.1	s__Salipiger aestuarii	78.22	394	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.58	99.38	0.94	0.92	5	-
GCF_014903745.1	s__Mangrovicoccus sp014903745	78.1759	417	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056725.1	s__Mangrovicoccus ximenensis	78.0987	406	1206	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mangrovicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:11,710] [INFO] GTDB search result was written to GCF_019061145.1_ASM1906114v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:11,711] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:11,716] [INFO] DFAST_QC result json was written to GCF_019061145.1_ASM1906114v1_genomic.fna/dqc_result.json
[2024-01-24 13:51:11,716] [INFO] DFAST_QC completed!
[2024-01-24 13:51:11,716] [INFO] Total running time: 0h1m39s