[2024-01-24 15:19:52,497] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:19:52,499] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:19:52,499] [INFO] DQC Reference Directory: /var/lib/cwl/stgc7eaf085-96fc-4392-a61a-a5693542ae21/dqc_reference
[2024-01-24 15:19:53,771] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:19:53,772] [INFO] Task started: Prodigal
[2024-01-24 15:19:53,773] [INFO] Running command: gunzip -c /var/lib/cwl/stg4bd7b391-85c0-46ff-a339-c7a632aac1b8/GCF_018200035.1_ASM1820003v1_genomic.fna.gz | prodigal -d GCF_018200035.1_ASM1820003v1_genomic.fna/cds.fna -a GCF_018200035.1_ASM1820003v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:20:07,291] [INFO] Task succeeded: Prodigal
[2024-01-24 15:20:07,292] [INFO] Task started: HMMsearch
[2024-01-24 15:20:07,292] [INFO] Running command: hmmsearch --tblout GCF_018200035.1_ASM1820003v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc7eaf085-96fc-4392-a61a-a5693542ae21/dqc_reference/reference_markers.hmm GCF_018200035.1_ASM1820003v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:20:07,602] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:20:07,604] [INFO] Found 6/6 markers.
[2024-01-24 15:20:07,646] [INFO] Query marker FASTA was written to GCF_018200035.1_ASM1820003v1_genomic.fna/markers.fasta
[2024-01-24 15:20:07,646] [INFO] Task started: Blastn
[2024-01-24 15:20:07,646] [INFO] Running command: blastn -query GCF_018200035.1_ASM1820003v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7eaf085-96fc-4392-a61a-a5693542ae21/dqc_reference/reference_markers.fasta -out GCF_018200035.1_ASM1820003v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:08,666] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:08,671] [INFO] Selected 29 target genomes.
[2024-01-24 15:20:08,671] [INFO] Target genome list was writen to GCF_018200035.1_ASM1820003v1_genomic.fna/target_genomes.txt
[2024-01-24 15:20:08,683] [INFO] Task started: fastANI
[2024-01-24 15:20:08,683] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bd7b391-85c0-46ff-a339-c7a632aac1b8/GCF_018200035.1_ASM1820003v1_genomic.fna.gz --refList GCF_018200035.1_ASM1820003v1_genomic.fna/target_genomes.txt --output GCF_018200035.1_ASM1820003v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:20:30,005] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:30,006] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc7eaf085-96fc-4392-a61a-a5693542ae21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:20:30,006] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc7eaf085-96fc-4392-a61a-a5693542ae21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:20:30,027] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:20:30,027] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:20:30,027] [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 sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	78.9476	608	1285	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	78.5899	457	1285	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	78.5759	466	1285	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	78.5434	542	1285	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	78.5221	536	1285	95	below_threshold
Sulfitobacter sediminilitoris	strain=JBTF-M27	GCA_010667575.1	2698830	2698830	type	True	78.2726	474	1285	95	below_threshold
Sulfitobacter dubius	strain=DSM 16472	GCA_900113435.1	218673	218673	type	True	78.1759	462	1285	95	below_threshold
Sulfitobacter maritimus	strain=S0837	GCA_013346665.1	2741719	2741719	type	True	78.1528	426	1285	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	78.1401	424	1285	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	78.1304	455	1285	95	below_threshold
Roseobacter cerasinus	strain=AI77	GCA_009811755.1	2602289	2602289	type	True	78.1259	453	1285	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	78.1237	426	1285	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	78.0274	396	1285	95	below_threshold
Thalassobius mangrovi	strain=GS-10	GCA_009857745.1	2692236	2692236	type	True	78.0085	407	1285	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	77.9966	488	1285	95	below_threshold
Sulfitobacter donghicola	strain=KCTC 12864	GCA_000622405.1	421000	421000	type	True	77.9448	380	1285	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	77.9302	398	1285	95	below_threshold
Sulfitobacter aestuariivivens	strain=TSTF-M16	GCA_014763045.1	2766981	2766981	type	True	77.9291	446	1285	95	below_threshold
Leisingera caerulea	strain=DSM 24564	GCA_000473325.1	506591	506591	type	True	77.8875	424	1285	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	77.8611	395	1285	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	77.7705	468	1285	95	below_threshold
Sulfitobacter donghicola	strain=JCM 14565	GCA_000712275.1	421000	421000	type	True	77.756	383	1285	95	below_threshold
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	77.7474	453	1285	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.3434	291	1285	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	77.2491	318	1285	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.227	257	1285	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	77.094	291	1285	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	76.9994	283	1285	95	below_threshold
Hasllibacter halocynthiae	strain=DSM 29318	GCA_003003095.1	595589	595589	type	True	76.8086	221	1285	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:20:30,029] [INFO] DFAST Taxonomy check result was written to GCF_018200035.1_ASM1820003v1_genomic.fna/tc_result.tsv
[2024-01-24 15:20:30,030] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:20:30,030] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:20:30,030] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc7eaf085-96fc-4392-a61a-a5693542ae21/dqc_reference/checkm_data
[2024-01-24 15:20:30,031] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:20:30,069] [INFO] Task started: CheckM
[2024-01-24 15:20:30,070] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018200035.1_ASM1820003v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018200035.1_ASM1820003v1_genomic.fna/checkm_input GCF_018200035.1_ASM1820003v1_genomic.fna/checkm_result
[2024-01-24 15:21:14,748] [INFO] Task succeeded: CheckM
[2024-01-24 15:21:14,749] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:21:14,770] [INFO] ===== Completeness check finished =====
[2024-01-24 15:21:14,770] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:21:14,770] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018200035.1_ASM1820003v1_genomic.fna/markers.fasta)
[2024-01-24 15:21:14,771] [INFO] Task started: Blastn
[2024-01-24 15:21:14,771] [INFO] Running command: blastn -query GCF_018200035.1_ASM1820003v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7eaf085-96fc-4392-a61a-a5693542ae21/dqc_reference/reference_markers_gtdb.fasta -out GCF_018200035.1_ASM1820003v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:21:16,679] [INFO] Task succeeded: Blastn
[2024-01-24 15:21:16,683] [INFO] Selected 21 target genomes.
[2024-01-24 15:21:16,683] [INFO] Target genome list was writen to GCF_018200035.1_ASM1820003v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:21:16,698] [INFO] Task started: fastANI
[2024-01-24 15:21:16,698] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bd7b391-85c0-46ff-a339-c7a632aac1b8/GCF_018200035.1_ASM1820003v1_genomic.fna.gz --refList GCF_018200035.1_ASM1820003v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018200035.1_ASM1820003v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:21:34,532] [INFO] Task succeeded: fastANI
[2024-01-24 15:21:34,552] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:21:34,553] [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_018200035.1	s__Sulfitobacter sp018200035	100.0	1285	1285	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	79.2253	633	1285	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	79.1478	626	1285	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	79.0422	597	1285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005887615.1	s__Sulfitobacter_E sabulilitoris	78.9451	607	1285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886735.1	s__Sulfitobacter alexandrii	78.8853	579	1285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003611275.1	s__Sulfitobacter sp001634775	78.7523	522	1285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.83	96.27	0.81	0.78	5	-
GCF_001634885.1	s__Sulfitobacter sp001634885	78.6173	462	1285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.85	95.06	0.84	0.78	4	-
GCF_000172095.1	s__Sulfitobacter indolifex	78.5444	457	1285	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	78.2645	475	1285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854855.1	s__Sulfitobacter sp017854855	78.209	477	1285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113435.1	s__Sulfitobacter dubius	78.1681	463	1285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.36	97.36	0.82	0.82	2	-
GCF_900129345.1	s__Ruegeria intermedia	78.1567	422	1285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015644665.1	s__Roseobacter sp015644665	78.1548	492	1285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013346665.1	s__Sulfitobacter maritimus	78.1499	427	1285	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	78.0238	433	1285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938215.1	s__Ruegeria sediminis	78.0184	397	1285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002210095.1	s__Marinibacterium profundimaris	77.98	466	1285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001507595.1	s__Ruegeria marisrubri	77.912	399	1285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002814095.1	s__Sagittula sp002814095	77.8696	403	1285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sagittula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003217735.2	s__Marinibacterium sp003217735	77.6717	453	1285	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 15:21:34,557] [INFO] GTDB search result was written to GCF_018200035.1_ASM1820003v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:21:34,558] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:21:34,563] [INFO] DFAST_QC result json was written to GCF_018200035.1_ASM1820003v1_genomic.fna/dqc_result.json
[2024-01-24 15:21:34,563] [INFO] DFAST_QC completed!
[2024-01-24 15:21:34,564] [INFO] Total running time: 0h1m42s