[2024-01-24 13:37:19,779] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:19,780] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:19,781] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d5550bd-17fe-4f26-b660-afd58193a09f/dqc_reference
[2024-01-24 13:37:21,114] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:21,115] [INFO] Task started: Prodigal
[2024-01-24 13:37:21,116] [INFO] Running command: gunzip -c /var/lib/cwl/stg9a578690-179a-4b1f-a917-1234350b357d/GCF_014763045.1_ASM1476304v1_genomic.fna.gz | prodigal -d GCF_014763045.1_ASM1476304v1_genomic.fna/cds.fna -a GCF_014763045.1_ASM1476304v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:36,178] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:36,178] [INFO] Task started: HMMsearch
[2024-01-24 13:37:36,178] [INFO] Running command: hmmsearch --tblout GCF_014763045.1_ASM1476304v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d5550bd-17fe-4f26-b660-afd58193a09f/dqc_reference/reference_markers.hmm GCF_014763045.1_ASM1476304v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:36,525] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:36,526] [INFO] Found 6/6 markers.
[2024-01-24 13:37:36,571] [INFO] Query marker FASTA was written to GCF_014763045.1_ASM1476304v1_genomic.fna/markers.fasta
[2024-01-24 13:37:36,572] [INFO] Task started: Blastn
[2024-01-24 13:37:36,572] [INFO] Running command: blastn -query GCF_014763045.1_ASM1476304v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d5550bd-17fe-4f26-b660-afd58193a09f/dqc_reference/reference_markers.fasta -out GCF_014763045.1_ASM1476304v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:37,346] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:37,354] [INFO] Selected 24 target genomes.
[2024-01-24 13:37:37,354] [INFO] Target genome list was writen to GCF_014763045.1_ASM1476304v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:37,367] [INFO] Task started: fastANI
[2024-01-24 13:37:37,367] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a578690-179a-4b1f-a917-1234350b357d/GCF_014763045.1_ASM1476304v1_genomic.fna.gz --refList GCF_014763045.1_ASM1476304v1_genomic.fna/target_genomes.txt --output GCF_014763045.1_ASM1476304v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:55,131] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:55,131] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d5550bd-17fe-4f26-b660-afd58193a09f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:55,132] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d5550bd-17fe-4f26-b660-afd58193a09f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:55,151] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:55,152] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:55,152] [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
Sulfitobacter aestuariivivens	strain=TSTF-M16	GCA_014763045.1	2766981	2766981	type	True	100.0	1391	1391	95	conclusive
Sulfitobacter maritimus	strain=S0837	GCA_013346665.1	2741719	2741719	type	True	78.0739	318	1391	95	below_threshold
Sulfitobacter sediminilitoris	strain=JBTF-M27	GCA_010667575.1	2698830	2698830	type	True	77.9449	456	1391	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	77.879	457	1391	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.8246	345	1391	95	below_threshold
Sulfitobacter geojensis	strain=MM-124	GCA_000622325.1	1342299	1342299	type	True	77.723	414	1391	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	77.7102	414	1391	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	77.6772	405	1391	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.6664	401	1391	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	77.6646	404	1391	95	below_threshold
Sulfitobacter dubius	strain=DSM 16472	GCA_900113435.1	218673	218673	type	True	77.6538	344	1391	95	below_threshold
Sulfitobacter noctilucicola	strain=NB-77	GCA_000622385.1	1342301	1342301	type	True	77.4307	376	1391	95	below_threshold
Sulfitobacter noctilucicola	strain=DSM 101015	GCA_014197555.1	1342301	1342301	type	True	77.3836	375	1391	95	below_threshold
Tateyamaria omphalii	strain=KCTC 12333	GCA_014651375.1	299262	299262	type	True	77.1955	292	1391	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	77.1805	335	1391	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	77.1513	283	1391	95	below_threshold
Sulfitobacter litoralis	strain=DSM 17584	GCA_900103185.1	335975	335975	type	True	77.1116	298	1391	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	77.0337	313	1391	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	76.9106	293	1391	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	76.8761	187	1391	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	76.8554	139	1391	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	76.8173	280	1391	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.6931	203	1391	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.5431	189	1391	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:55,154] [INFO] DFAST Taxonomy check result was written to GCF_014763045.1_ASM1476304v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:55,155] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:55,155] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:55,156] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d5550bd-17fe-4f26-b660-afd58193a09f/dqc_reference/checkm_data
[2024-01-24 13:37:55,158] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:55,208] [INFO] Task started: CheckM
[2024-01-24 13:37:55,208] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014763045.1_ASM1476304v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014763045.1_ASM1476304v1_genomic.fna/checkm_input GCF_014763045.1_ASM1476304v1_genomic.fna/checkm_result
[2024-01-24 13:38:39,583] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:39,585] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:39,604] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:39,605] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:39,605] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014763045.1_ASM1476304v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:39,606] [INFO] Task started: Blastn
[2024-01-24 13:38:39,606] [INFO] Running command: blastn -query GCF_014763045.1_ASM1476304v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d5550bd-17fe-4f26-b660-afd58193a09f/dqc_reference/reference_markers_gtdb.fasta -out GCF_014763045.1_ASM1476304v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:40,650] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:40,654] [INFO] Selected 20 target genomes.
[2024-01-24 13:38:40,654] [INFO] Target genome list was writen to GCF_014763045.1_ASM1476304v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:40,698] [INFO] Task started: fastANI
[2024-01-24 13:38:40,698] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a578690-179a-4b1f-a917-1234350b357d/GCF_014763045.1_ASM1476304v1_genomic.fna.gz --refList GCF_014763045.1_ASM1476304v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014763045.1_ASM1476304v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:56,108] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:56,127] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:56,127] [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_014763045.1	s__Sulfitobacter aestuariivivens	100.0	1391	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003335585.1	s__Sulfitobacter sp003335585	78.3389	564	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650875.1	s__Sulfitobacter sp001650875	78.2257	532	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363555.1	s__Sulfitobacter sp009363555	78.146	495	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010667575.1	s__Sulfitobacter sediminilitoris	77.9286	455	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016801775.1	s__Sulfitobacter mediterraneus_A	77.8967	470	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	99.99	1.00	1.00	16	-
GCF_001886735.1	s__Sulfitobacter alexandrii	77.8719	452	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335545.1	s__Ascidiaceihabitans sp003335545	77.8565	377	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352065.1	s__Sulfitobacter sp003352065	77.833	387	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743885.1	s__Sulfitobacter sp001635605	77.8173	395	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	98.54	95.97	0.90	0.86	4	-
GCA_017854855.1	s__Sulfitobacter sp017854855	77.8084	474	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002405.1	s__Sulfitobacter sp013002405	77.6977	386	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622365.1	s__Sulfitobacter noctilucae	77.6693	406	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015644665.1	s__Roseobacter sp015644665	77.5741	387	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013282155.1	s__Sulfitobacter sp013282155	77.4994	353	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.41	99.36	0.93	0.90	3	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	77.3545	331	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_000511355.1	s__Leisingera methylohalidivorans	77.141	282	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	77.0337	313	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013139555.1	s__Sulfitobacter sp013139555	77.031	249	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101475.1	s__Ruegeria_B marina	76.8173	280	1391	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:56,130] [INFO] GTDB search result was written to GCF_014763045.1_ASM1476304v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:56,130] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:56,138] [INFO] DFAST_QC result json was written to GCF_014763045.1_ASM1476304v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:56,138] [INFO] DFAST_QC completed!
[2024-01-24 13:38:56,139] [INFO] Total running time: 0h1m36s