[2024-01-24 14:14:37,586] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:37,589] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:37,590] [INFO] DQC Reference Directory: /var/lib/cwl/stg58ef1614-b175-400c-ab84-919c42ca77f6/dqc_reference
[2024-01-24 14:14:39,059] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:39,060] [INFO] Task started: Prodigal
[2024-01-24 14:14:39,060] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ce7f6a0-3ff2-4781-9975-349c5705483a/GCF_009650435.1_ASM965043v1_genomic.fna.gz | prodigal -d GCF_009650435.1_ASM965043v1_genomic.fna/cds.fna -a GCF_009650435.1_ASM965043v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:14,318] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:14,319] [INFO] Task started: HMMsearch
[2024-01-24 14:15:14,319] [INFO] Running command: hmmsearch --tblout GCF_009650435.1_ASM965043v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58ef1614-b175-400c-ab84-919c42ca77f6/dqc_reference/reference_markers.hmm GCF_009650435.1_ASM965043v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:14,696] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:14,698] [INFO] Found 6/6 markers.
[2024-01-24 14:15:14,753] [INFO] Query marker FASTA was written to GCF_009650435.1_ASM965043v1_genomic.fna/markers.fasta
[2024-01-24 14:15:14,754] [INFO] Task started: Blastn
[2024-01-24 14:15:14,754] [INFO] Running command: blastn -query GCF_009650435.1_ASM965043v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58ef1614-b175-400c-ab84-919c42ca77f6/dqc_reference/reference_markers.fasta -out GCF_009650435.1_ASM965043v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:15,398] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:15,404] [INFO] Selected 24 target genomes.
[2024-01-24 14:15:15,405] [INFO] Target genome list was writen to GCF_009650435.1_ASM965043v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:15,416] [INFO] Task started: fastANI
[2024-01-24 14:15:15,416] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ce7f6a0-3ff2-4781-9975-349c5705483a/GCF_009650435.1_ASM965043v1_genomic.fna.gz --refList GCF_009650435.1_ASM965043v1_genomic.fna/target_genomes.txt --output GCF_009650435.1_ASM965043v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:40,841] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:40,842] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58ef1614-b175-400c-ab84-919c42ca77f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:40,842] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58ef1614-b175-400c-ab84-919c42ca77f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:40,931] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:15:40,932] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:40,932] [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
Foetidibacter luteolus	strain=YG09	GCA_009650435.1	2608880	2608880	type	True	100.0	2373	2381	95	conclusive
Panacibacter microcysteis	strain=DH6	GCA_015831355.1	2793269	2793269	type	True	76.7646	217	2381	95	below_threshold
Ferruginibacter albus	strain=KIS38-8	GCA_020042285.1	2875540	2875540	type	True	76.711	52	2381	95	below_threshold
Deminuibacter soli	strain=K23C18032701	GCA_003412455.1	2291815	2291815	type	True	76.4646	191	2381	95	below_threshold
Filimonas lacunae	strain=NBRC 104114	GCA_002355595.1	477680	477680	type	True	76.4259	151	2381	95	below_threshold
Hydrotalea sandarakina	strain=DSM 23241	GCA_003254115.1	1004304	1004304	type	True	76.3583	63	2381	95	below_threshold
Sediminibacterium roseum	strain=SYL130	GCA_009939005.1	1978412	1978412	type	True	76.3033	76	2381	95	below_threshold
Ilyomonas limi	strain=17mud1-8	GCA_005233845.1	2575867	2575867	type	True	76.2081	149	2381	95	below_threshold
Parafilimonas terrae	strain=DSM 28286	GCA_900115755.1	1465490	1465490	type	True	76.2049	164	2381	95	below_threshold
Panacibacter ginsenosidivorans	strain=Gsoil1550	GCA_007971225.1	1813871	1813871	type	True	76.1939	167	2381	95	below_threshold
Filimonas zeae	strain=CGMCC 1.15290	GCA_014641615.1	1737353	1737353	type	True	76.1673	168	2381	95	below_threshold
Filimonas lacunae	strain=DSM 21054	GCA_900156765.1	477680	477680	type	True	76.1603	147	2381	95	below_threshold
Segetibacter koreensis	strain=DSM 18137	GCA_000374045.1	398037	398037	type	True	76.1177	68	2381	95	below_threshold
Limnovirga soli	strain=KCS-6	GCA_013106755.1	2656915	2656915	type	True	76.0889	164	2381	95	below_threshold
Chitinophaga vietnamensis	strain=BD 01	GCA_902167635.1	2593957	2593957	type	True	76.0171	60	2381	95	below_threshold
Hydrotalea flava	strain=CCUG 51397	GCA_001623405.1	714549	714549	suspected-type	True	75.9154	75	2381	95	below_threshold
Hydrotalea lipotrueae	strain=TMF_100	GCA_019249625.1	2803817	2803817	type	True	75.7803	80	2381	95	below_threshold
Filimonas effusa	strain=TTM-71	GCA_004118675.1	2508721	2508721	type	True	75.7342	106	2381	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:40,934] [INFO] DFAST Taxonomy check result was written to GCF_009650435.1_ASM965043v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:40,934] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:40,934] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:40,934] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58ef1614-b175-400c-ab84-919c42ca77f6/dqc_reference/checkm_data
[2024-01-24 14:15:40,940] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:41,010] [INFO] Task started: CheckM
[2024-01-24 14:15:41,010] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009650435.1_ASM965043v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009650435.1_ASM965043v1_genomic.fna/checkm_input GCF_009650435.1_ASM965043v1_genomic.fna/checkm_result
[2024-01-24 14:17:20,475] [INFO] Task succeeded: CheckM
[2024-01-24 14:17:20,477] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:17:20,502] [INFO] ===== Completeness check finished =====
[2024-01-24 14:17:20,503] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:17:20,503] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009650435.1_ASM965043v1_genomic.fna/markers.fasta)
[2024-01-24 14:17:20,504] [INFO] Task started: Blastn
[2024-01-24 14:17:20,504] [INFO] Running command: blastn -query GCF_009650435.1_ASM965043v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58ef1614-b175-400c-ab84-919c42ca77f6/dqc_reference/reference_markers_gtdb.fasta -out GCF_009650435.1_ASM965043v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:17:21,512] [INFO] Task succeeded: Blastn
[2024-01-24 14:17:21,515] [INFO] Selected 25 target genomes.
[2024-01-24 14:17:21,515] [INFO] Target genome list was writen to GCF_009650435.1_ASM965043v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:17:21,562] [INFO] Task started: fastANI
[2024-01-24 14:17:21,562] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ce7f6a0-3ff2-4781-9975-349c5705483a/GCF_009650435.1_ASM965043v1_genomic.fna.gz --refList GCF_009650435.1_ASM965043v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009650435.1_ASM965043v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:17:50,622] [INFO] Task succeeded: fastANI
[2024-01-24 14:17:50,660] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:17:50,661] [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_009650435.1	s__Foetidibacter luteolus	100.0	2371	2381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Foetidibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000515315.1	s__Sediminibacterium sp000515315	76.5489	98	2381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	96.66	96.66	0.84	0.84	2	-
GCF_003412455.1	s__Deminuibacter soli	76.4646	191	2381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Deminuibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254115.1	s__Hydrotalea sandarakina	76.3819	62	2381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Hydrotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004361915.1	s__Sediminibacterium goheungense	76.3049	85	2381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903882935.1	s__JABDFW01 sp903882935	76.2818	160	2381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JABDFW01	95.0	99.98	99.96	0.98	0.97	5	-
GCA_013285915.1	s__JABDFW01 sp013285915	76.2178	118	2381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JABDFW01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007994055.1	s__Filimonas endophytica	76.2036	154	2381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Filimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007971225.1	s__Panacibacter ginsenosidivorans	76.1988	169	2381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Panacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641615.1	s__Filimonas zeae	76.1569	169	2381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Filimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002390845.1	s__Panacibacter sp002390845	76.1556	195	2381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Panacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017306865.1	s__JAFKHH01 sp017306865	76.1112	119	2381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JAFKHH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013106755.1	s__Panacibacter sp013106755	76.1056	162	2381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Panacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003097095.1	s__Filimonas sp003097095	76.0638	162	2381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Filimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002973575.1	s__Sediminibacterium magnilacihabitans	75.9934	106	2381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	99.08	98.17	0.92	0.85	3	-
GCA_016192105.1	s__JJ008 sp016192105	75.9923	60	2381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004028765.1	s__Sediminibacterium sp004028765	75.9389	92	2381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001623405.1	s__Hydrotalea flava	75.9154	75	2381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Hydrotalea	95.0	95.88	95.18	0.90	0.86	13	-
GCA_903884185.1	s__CAILAF01 sp903884185	75.882	58	2381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAILAF01	95.0	99.92	99.92	0.95	0.95	2	-
GCA_013289015.1	s__Parafilimonas sp013289015	75.5205	61	2381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Parafilimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903642275.1	s__Parafilimonas sp903642275	75.2878	76	2381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Parafilimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:17:50,663] [INFO] GTDB search result was written to GCF_009650435.1_ASM965043v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:17:50,663] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:17:50,667] [INFO] DFAST_QC result json was written to GCF_009650435.1_ASM965043v1_genomic.fna/dqc_result.json
[2024-01-24 14:17:50,668] [INFO] DFAST_QC completed!
[2024-01-24 14:17:50,668] [INFO] Total running time: 0h3m13s