[2024-01-24 13:41:20,268] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:20,270] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:20,270] [INFO] DQC Reference Directory: /var/lib/cwl/stg2207ba0a-5cdb-4730-a9e7-d4859c5b1098/dqc_reference
[2024-01-24 13:41:21,664] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:21,665] [INFO] Task started: Prodigal
[2024-01-24 13:41:21,666] [INFO] Running command: gunzip -c /var/lib/cwl/stg90185654-9ca5-4572-8ab5-e399dcf37e40/GCF_013407805.1_ASM1340780v1_genomic.fna.gz | prodigal -d GCF_013407805.1_ASM1340780v1_genomic.fna/cds.fna -a GCF_013407805.1_ASM1340780v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:37,348] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:37,349] [INFO] Task started: HMMsearch
[2024-01-24 13:41:37,349] [INFO] Running command: hmmsearch --tblout GCF_013407805.1_ASM1340780v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2207ba0a-5cdb-4730-a9e7-d4859c5b1098/dqc_reference/reference_markers.hmm GCF_013407805.1_ASM1340780v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:37,650] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:37,651] [INFO] Found 6/6 markers.
[2024-01-24 13:41:37,690] [INFO] Query marker FASTA was written to GCF_013407805.1_ASM1340780v1_genomic.fna/markers.fasta
[2024-01-24 13:41:37,691] [INFO] Task started: Blastn
[2024-01-24 13:41:37,691] [INFO] Running command: blastn -query GCF_013407805.1_ASM1340780v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2207ba0a-5cdb-4730-a9e7-d4859c5b1098/dqc_reference/reference_markers.fasta -out GCF_013407805.1_ASM1340780v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:38,505] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:38,508] [INFO] Selected 15 target genomes.
[2024-01-24 13:41:38,509] [INFO] Target genome list was writen to GCF_013407805.1_ASM1340780v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:38,521] [INFO] Task started: fastANI
[2024-01-24 13:41:38,521] [INFO] Running command: fastANI --query /var/lib/cwl/stg90185654-9ca5-4572-8ab5-e399dcf37e40/GCF_013407805.1_ASM1340780v1_genomic.fna.gz --refList GCF_013407805.1_ASM1340780v1_genomic.fna/target_genomes.txt --output GCF_013407805.1_ASM1340780v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:50,508] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:50,508] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2207ba0a-5cdb-4730-a9e7-d4859c5b1098/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:50,508] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2207ba0a-5cdb-4730-a9e7-d4859c5b1098/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:50,522] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:50,522] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:50,523] [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 geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	100.0	1401	1401	95	conclusive
Sulfitobacter geojensis	strain=MM-124	GCA_000622325.1	1342299	1342299	type	True	99.9975	1399	1401	95	conclusive
Sulfitobacter noctilucicola	strain=NB-77	GCA_000622385.1	1342301	1342301	type	True	81.207	666	1401	95	below_threshold
Sulfitobacter noctilucicola	strain=DSM 101015	GCA_014197555.1	1342301	1342301	type	True	81.1644	656	1401	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	79.2766	652	1401	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	78.5286	572	1401	95	below_threshold
Sulfitobacter litoralis	strain=DSM 17584	GCA_900103185.1	335975	335975	type	True	78.3894	416	1401	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	78.1843	485	1401	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	78.1332	476	1401	95	below_threshold
Sulfitobacter aestuariivivens	strain=TSTF-M16	GCA_014763045.1	2766981	2766981	type	True	77.6741	423	1401	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	76.7802	170	1401	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	76.6976	205	1401	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	76.6097	179	1401	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	76.5048	141	1401	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	76.5011	205	1401	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:50,524] [INFO] DFAST Taxonomy check result was written to GCF_013407805.1_ASM1340780v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:50,525] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:50,525] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:50,525] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2207ba0a-5cdb-4730-a9e7-d4859c5b1098/dqc_reference/checkm_data
[2024-01-24 13:41:50,527] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:50,568] [INFO] Task started: CheckM
[2024-01-24 13:41:50,568] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013407805.1_ASM1340780v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013407805.1_ASM1340780v1_genomic.fna/checkm_input GCF_013407805.1_ASM1340780v1_genomic.fna/checkm_result
[2024-01-24 13:42:37,000] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:37,002] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:37,027] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:37,028] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:37,028] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013407805.1_ASM1340780v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:37,029] [INFO] Task started: Blastn
[2024-01-24 13:42:37,029] [INFO] Running command: blastn -query GCF_013407805.1_ASM1340780v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2207ba0a-5cdb-4730-a9e7-d4859c5b1098/dqc_reference/reference_markers_gtdb.fasta -out GCF_013407805.1_ASM1340780v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:38,119] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:38,123] [INFO] Selected 17 target genomes.
[2024-01-24 13:42:38,123] [INFO] Target genome list was writen to GCF_013407805.1_ASM1340780v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:38,133] [INFO] Task started: fastANI
[2024-01-24 13:42:38,133] [INFO] Running command: fastANI --query /var/lib/cwl/stg90185654-9ca5-4572-8ab5-e399dcf37e40/GCF_013407805.1_ASM1340780v1_genomic.fna.gz --refList GCF_013407805.1_ASM1340780v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013407805.1_ASM1340780v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:51,884] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:51,909] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:51,909] [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_000622325.1	s__Sulfitobacter geojensis	99.9975	1399	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.34	96.22	0.90	0.89	35	conclusive
GCF_000622385.1	s__Sulfitobacter noctilucicola	81.2069	666	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000622365.1	s__Sulfitobacter noctilucae	79.2716	652	1401	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	79.2071	631	1401	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	78.9153	573	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	99.99	1.00	1.00	16	-
GCF_001650875.1	s__Sulfitobacter sp001650875	78.6561	571	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335585.1	s__Sulfitobacter sp003335585	78.6418	597	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054325.1	s__Sulfitobacter mediterraneus	78.5216	573	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.52	96.39	0.88	0.86	71	-
GCF_010667575.1	s__Sulfitobacter sediminilitoris	78.4926	564	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103185.1	s__Sulfitobacter litoralis	78.3894	416	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.10	98.53	0.92	0.85	6	-
GCA_013139555.1	s__Sulfitobacter sp013139555	78.2797	369	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	78.1999	483	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_003335545.1	s__Ascidiaceihabitans sp003335545	78.1142	485	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886735.1	s__Sulfitobacter alexandrii	77.8923	442	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	77.7607	473	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196805.1	s__Sulfitobacter undariae	77.7109	320	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009789075.1	s__Pseudooceanicola pacificus	76.6926	170	1401	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:51,911] [INFO] GTDB search result was written to GCF_013407805.1_ASM1340780v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:51,911] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:51,915] [INFO] DFAST_QC result json was written to GCF_013407805.1_ASM1340780v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:51,915] [INFO] DFAST_QC completed!
[2024-01-24 13:42:51,915] [INFO] Total running time: 0h1m32s