[2023-06-28 10:57:09,149] [INFO] DFAST_QC pipeline started.
[2023-06-28 10:57:09,156] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 10:57:09,156] [INFO] DQC Reference Directory: /var/lib/cwl/stg078bf928-c992-4cb6-99ed-8677a4db6a9d/dqc_reference
[2023-06-28 10:57:10,534] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 10:57:10,535] [INFO] Task started: Prodigal
[2023-06-28 10:57:10,536] [INFO] Running command: gunzip -c /var/lib/cwl/stg4c1dc42c-8c88-4dcf-a907-efd78f9e4538/GCA_002708965.1_ASM270896v1_genomic.fna.gz | prodigal -d GCA_002708965.1_ASM270896v1_genomic.fna/cds.fna -a GCA_002708965.1_ASM270896v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 10:57:22,450] [INFO] Task succeeded: Prodigal
[2023-06-28 10:57:22,450] [INFO] Task started: HMMsearch
[2023-06-28 10:57:22,450] [INFO] Running command: hmmsearch --tblout GCA_002708965.1_ASM270896v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg078bf928-c992-4cb6-99ed-8677a4db6a9d/dqc_reference/reference_markers.hmm GCA_002708965.1_ASM270896v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 10:57:22,728] [INFO] Task succeeded: HMMsearch
[2023-06-28 10:57:22,729] [INFO] Found 6/6 markers.
[2023-06-28 10:57:22,774] [INFO] Query marker FASTA was written to GCA_002708965.1_ASM270896v1_genomic.fna/markers.fasta
[2023-06-28 10:57:22,775] [INFO] Task started: Blastn
[2023-06-28 10:57:22,775] [INFO] Running command: blastn -query GCA_002708965.1_ASM270896v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg078bf928-c992-4cb6-99ed-8677a4db6a9d/dqc_reference/reference_markers.fasta -out GCA_002708965.1_ASM270896v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:57:23,466] [INFO] Task succeeded: Blastn
[2023-06-28 10:57:23,470] [INFO] Selected 22 target genomes.
[2023-06-28 10:57:23,470] [INFO] Target genome list was writen to GCA_002708965.1_ASM270896v1_genomic.fna/target_genomes.txt
[2023-06-28 10:57:23,479] [INFO] Task started: fastANI
[2023-06-28 10:57:23,479] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c1dc42c-8c88-4dcf-a907-efd78f9e4538/GCA_002708965.1_ASM270896v1_genomic.fna.gz --refList GCA_002708965.1_ASM270896v1_genomic.fna/target_genomes.txt --output GCA_002708965.1_ASM270896v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 10:57:41,029] [INFO] Task succeeded: fastANI
[2023-06-28 10:57:41,029] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg078bf928-c992-4cb6-99ed-8677a4db6a9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 10:57:41,030] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg078bf928-c992-4cb6-99ed-8677a4db6a9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 10:57:41,046] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 10:57:41,047] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 10:57:41,047] [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 pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	80.8766	475	1162	95	below_threshold
Sulfitobacter litoralis	strain=DSM 17584	GCA_900103185.1	335975	335975	type	True	80.4438	448	1162	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	79.7254	288	1162	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	79.7185	282	1162	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	78.958	387	1162	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	77.8457	247	1162	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.7985	252	1162	95	below_threshold
Sulfitobacter dubius	strain=DSM 16472	GCA_900113435.1	218673	218673	type	True	77.6781	242	1162	95	below_threshold
Sulfitobacter geojensis	strain=MM-124	GCA_000622325.1	1342299	1342299	type	True	77.5618	245	1162	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	77.5533	241	1162	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	77.306	154	1162	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	77.2558	232	1162	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	77.2398	263	1162	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	77.2006	269	1162	95	below_threshold
Sulfitobacter sediminilitoris	strain=JBTF-M27	GCA_010667575.1	2698830	2698830	type	True	77.1757	213	1162	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	76.9781	169	1162	95	below_threshold
Antarcticimicrobium sediminis	strain=S4J41	GCA_004348975.1	2546227	2546227	type	True	76.8219	185	1162	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.6439	109	1162	95	below_threshold
Ruegeria atlantica	strain=CECT 4292	GCA_001458195.1	81569	81569	suspected-type	True	76.4529	131	1162	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	76.0698	93	1162	95	below_threshold
Pseudogemmobacter bohemicus	strain=Cd-10	GCA_003290025.1	2250708	2250708	type	True	76.0177	79	1162	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 10:57:41,049] [INFO] DFAST Taxonomy check result was written to GCA_002708965.1_ASM270896v1_genomic.fna/tc_result.tsv
[2023-06-28 10:57:41,050] [INFO] ===== Taxonomy check completed =====
[2023-06-28 10:57:41,050] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 10:57:41,050] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg078bf928-c992-4cb6-99ed-8677a4db6a9d/dqc_reference/checkm_data
[2023-06-28 10:57:41,051] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 10:57:41,095] [INFO] Task started: CheckM
[2023-06-28 10:57:41,095] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002708965.1_ASM270896v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002708965.1_ASM270896v1_genomic.fna/checkm_input GCA_002708965.1_ASM270896v1_genomic.fna/checkm_result
[2023-06-28 10:58:18,852] [INFO] Task succeeded: CheckM
[2023-06-28 10:58:18,853] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 10:58:18,877] [INFO] ===== Completeness check finished =====
[2023-06-28 10:58:18,877] [INFO] ===== Start GTDB Search =====
[2023-06-28 10:58:18,877] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002708965.1_ASM270896v1_genomic.fna/markers.fasta)
[2023-06-28 10:58:18,878] [INFO] Task started: Blastn
[2023-06-28 10:58:18,878] [INFO] Running command: blastn -query GCA_002708965.1_ASM270896v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg078bf928-c992-4cb6-99ed-8677a4db6a9d/dqc_reference/reference_markers_gtdb.fasta -out GCA_002708965.1_ASM270896v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:58:19,898] [INFO] Task succeeded: Blastn
[2023-06-28 10:58:19,904] [INFO] Selected 12 target genomes.
[2023-06-28 10:58:19,904] [INFO] Target genome list was writen to GCA_002708965.1_ASM270896v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 10:58:19,927] [INFO] Task started: fastANI
[2023-06-28 10:58:19,927] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c1dc42c-8c88-4dcf-a907-efd78f9e4538/GCA_002708965.1_ASM270896v1_genomic.fna.gz --refList GCA_002708965.1_ASM270896v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002708965.1_ASM270896v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 10:58:30,144] [INFO] Task succeeded: fastANI
[2023-06-28 10:58:30,164] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 10:58:30,165] [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_002731875.1	s__Sulfitobacter sp002731875	99.9315	1105	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.91	99.88	0.91	0.87	3	conclusive
GCA_011050655.1	s__Sulfitobacter sp011050655	86.5769	823	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106935.1	s__Sulfitobacter pontiacus	80.8766	475	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.43	97.01	0.92	0.86	24	-
GCF_900103185.1	s__Sulfitobacter litoralis	80.4573	447	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.10	98.53	0.92	0.85	6	-
GCF_006064855.1	s__Sulfitobacter sp006064855	79.8969	434	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013282155.1	s__Sulfitobacter sp013282155	79.5407	474	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.41	99.36	0.93	0.90	3	-
GCF_000156335.1	s__Sulfitobacter sp000156335	79.0786	468	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013139555.1	s__Sulfitobacter sp013139555	78.9615	369	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	77.7697	251	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_000622325.1	s__Sulfitobacter geojensis	77.5618	245	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.34	96.22	0.90	0.89	35	-
GCA_003217735.2	s__Marinibacterium sp003217735	77.2433	172	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
GCF_900143525.1	s__Ruegeria sp900143525	76.9238	123	1162	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 10:58:30,167] [INFO] GTDB search result was written to GCA_002708965.1_ASM270896v1_genomic.fna/result_gtdb.tsv
[2023-06-28 10:58:30,168] [INFO] ===== GTDB Search completed =====
[2023-06-28 10:58:30,172] [INFO] DFAST_QC result json was written to GCA_002708965.1_ASM270896v1_genomic.fna/dqc_result.json
[2023-06-28 10:58:30,172] [INFO] DFAST_QC completed!
[2023-06-28 10:58:30,172] [INFO] Total running time: 0h1m21s