[2024-01-24 11:58:57,294] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:57,298] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:57,298] [INFO] DQC Reference Directory: /var/lib/cwl/stg38056ada-8684-4ff0-aec4-144cbc72bb7b/dqc_reference
[2024-01-24 11:58:58,660] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:58,661] [INFO] Task started: Prodigal
[2024-01-24 11:58:58,661] [INFO] Running command: gunzip -c /var/lib/cwl/stg82707332-e9ab-454c-b528-82a1ea91c3e7/GCF_015831355.1_ASM1583135v1_genomic.fna.gz | prodigal -d GCF_015831355.1_ASM1583135v1_genomic.fna/cds.fna -a GCF_015831355.1_ASM1583135v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:25,611] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:25,611] [INFO] Task started: HMMsearch
[2024-01-24 11:59:25,611] [INFO] Running command: hmmsearch --tblout GCF_015831355.1_ASM1583135v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg38056ada-8684-4ff0-aec4-144cbc72bb7b/dqc_reference/reference_markers.hmm GCF_015831355.1_ASM1583135v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:25,935] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:25,936] [INFO] Found 6/6 markers.
[2024-01-24 11:59:25,976] [INFO] Query marker FASTA was written to GCF_015831355.1_ASM1583135v1_genomic.fna/markers.fasta
[2024-01-24 11:59:25,976] [INFO] Task started: Blastn
[2024-01-24 11:59:25,977] [INFO] Running command: blastn -query GCF_015831355.1_ASM1583135v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38056ada-8684-4ff0-aec4-144cbc72bb7b/dqc_reference/reference_markers.fasta -out GCF_015831355.1_ASM1583135v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:26,663] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:26,667] [INFO] Selected 22 target genomes.
[2024-01-24 11:59:26,667] [INFO] Target genome list was writen to GCF_015831355.1_ASM1583135v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:26,676] [INFO] Task started: fastANI
[2024-01-24 11:59:26,676] [INFO] Running command: fastANI --query /var/lib/cwl/stg82707332-e9ab-454c-b528-82a1ea91c3e7/GCF_015831355.1_ASM1583135v1_genomic.fna.gz --refList GCF_015831355.1_ASM1583135v1_genomic.fna/target_genomes.txt --output GCF_015831355.1_ASM1583135v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:46,750] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:46,751] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg38056ada-8684-4ff0-aec4-144cbc72bb7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:46,751] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg38056ada-8684-4ff0-aec4-144cbc72bb7b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:46,764] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:46,765] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:46,765] [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
Panacibacter microcysteis	strain=DH6	GCA_015831355.1	2793269	2793269	type	True	100.0	1729	1731	95	conclusive
Panacibacter ginsenosidivorans	strain=Gsoil1550	GCA_007971225.1	1813871	1813871	type	True	78.0025	563	1731	95	below_threshold
Foetidibacter luteolus	strain=YG09	GCA_009650435.1	2608880	2608880	type	True	76.7029	213	1731	95	below_threshold
Flavisolibacter tropicus	strain=LCS9	GCA_001644645.1	1492898	1492898	type	True	76.6192	63	1731	95	below_threshold
Paraflavitalea soli	strain=5GH32-13	GCA_003555545.1	2315862	2315862	type	True	76.5982	66	1731	95	below_threshold
Filimonas lacunae	strain=NBRC 104114	GCA_002355595.1	477680	477680	type	True	76.5758	101	1731	95	below_threshold
Phnomibacter ginsenosidimutans	strain=SB-02	GCA_009740285.1	2676868	2676868	type	True	76.5422	71	1731	95	below_threshold
Deminuibacter soli	strain=K23C18032701	GCA_003412455.1	2291815	2291815	type	True	76.367	150	1731	95	below_threshold
Flavisolibacter ginsengisoli	strain=DSM 18119	GCA_900129295.1	462367	462367	type	True	76.3287	61	1731	95	below_threshold
Limnovirga soli	strain=KCS-6	GCA_013106755.1	2656915	2656915	type	True	76.2561	216	1731	95	below_threshold
Ferruginibacter albus	strain=KIS38-8	GCA_020042285.1	2875540	2875540	type	True	76.236	68	1731	95	below_threshold
Filimonas lacunae	strain=DSM 21054	GCA_900156765.1	477680	477680	type	True	76.2184	97	1731	95	below_threshold
Sediminibacterium soli	strain=WSJ-3	GCA_009939225.1	2698829	2698829	type	True	76.1705	73	1731	95	below_threshold
Ilyomonas limi	strain=17mud1-8	GCA_005233845.1	2575867	2575867	type	True	76.141	111	1731	95	below_threshold
Pinibacter aurantiacus	strain=MAH-26	GCA_019130065.1	2851599	2851599	type	True	76.1091	69	1731	95	below_threshold
Hydrotalea flava	strain=CCUG 51397	GCA_001623405.1	714549	714549	suspected-type	True	76.0238	57	1731	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:46,766] [INFO] DFAST Taxonomy check result was written to GCF_015831355.1_ASM1583135v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:46,767] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:46,767] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:46,767] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg38056ada-8684-4ff0-aec4-144cbc72bb7b/dqc_reference/checkm_data
[2024-01-24 11:59:46,768] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:46,818] [INFO] Task started: CheckM
[2024-01-24 11:59:46,819] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015831355.1_ASM1583135v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015831355.1_ASM1583135v1_genomic.fna/checkm_input GCF_015831355.1_ASM1583135v1_genomic.fna/checkm_result
[2024-01-24 12:00:55,195] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:55,196] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:55,216] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:55,216] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:55,216] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015831355.1_ASM1583135v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:55,217] [INFO] Task started: Blastn
[2024-01-24 12:00:55,217] [INFO] Running command: blastn -query GCF_015831355.1_ASM1583135v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg38056ada-8684-4ff0-aec4-144cbc72bb7b/dqc_reference/reference_markers_gtdb.fasta -out GCF_015831355.1_ASM1583135v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:56,238] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:56,242] [INFO] Selected 22 target genomes.
[2024-01-24 12:00:56,242] [INFO] Target genome list was writen to GCF_015831355.1_ASM1583135v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:56,268] [INFO] Task started: fastANI
[2024-01-24 12:00:56,268] [INFO] Running command: fastANI --query /var/lib/cwl/stg82707332-e9ab-454c-b528-82a1ea91c3e7/GCF_015831355.1_ASM1583135v1_genomic.fna.gz --refList GCF_015831355.1_ASM1583135v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015831355.1_ASM1583135v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:01:12,810] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:12,824] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:01:12,824] [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_015831355.1	s__Panacibacter sp015831355	100.0	1729	1731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Panacibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007971225.1	s__Panacibacter ginsenosidivorans	78.0091	560	1731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Panacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009650435.1	s__Foetidibacter luteolus	76.7979	212	1731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Foetidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017306865.1	s__JAFKHH01 sp017306865	76.7865	101	1731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JAFKHH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002478885.1	s__Panacibacter sp002478885	76.5662	199	1731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Panacibacter	95.0	99.95	99.95	0.95	0.95	2	-
GCA_002390845.1	s__Panacibacter sp002390845	76.399	283	1731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Panacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129295.1	s__Flavisolibacter ginsengisoli	76.3605	61	1731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013106755.1	s__Panacibacter sp013106755	76.2642	215	1731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Panacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014163555.1	s__Flavisolibacter sp014163555	76.2509	63	1731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002337125.1	s__Lacibacter sp002337125	76.2491	93	1731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Lacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001302245.1	s__PMP191F sp001302245	76.1412	97	1731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__PMP191F	95.0	99.37	99.37	0.95	0.95	2	-
GCF_005233845.1	s__Ilyomonas limi	76.141	111	1731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ilyomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001623405.1	s__Hydrotalea flava	76.0238	57	1731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Hydrotalea	95.0	95.88	95.18	0.90	0.86	13	-
GCA_004297075.1	s__Sediminibacterium sp004297075	75.9166	59	1731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	98.05	98.05	0.89	0.89	2	-
GCA_903882935.1	s__JABDFW01 sp903882935	75.8407	76	1731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JABDFW01	95.0	99.98	99.96	0.98	0.97	5	-
GCA_018268035.1	s__Parafilimonas sp018268035	75.727	98	1731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Parafilimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903830285.1	s__CAILAF01 sp903830285	75.6628	67	1731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__CAILAF01	95.0	99.59	99.53	0.91	0.89	4	-
GCA_003526435.1	s__Sediminibacterium sp003526435	75.5906	50	1731	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:01:12,826] [INFO] GTDB search result was written to GCF_015831355.1_ASM1583135v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:01:12,826] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:01:12,830] [INFO] DFAST_QC result json was written to GCF_015831355.1_ASM1583135v1_genomic.fna/dqc_result.json
[2024-01-24 12:01:12,830] [INFO] DFAST_QC completed!
[2024-01-24 12:01:12,830] [INFO] Total running time: 0h2m16s