[2023-06-28 20:49:43,985] [INFO] DFAST_QC pipeline started.
[2023-06-28 20:49:43,987] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 20:49:43,987] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e9fb72a-8246-4b3a-ae97-9d079573691e/dqc_reference
[2023-06-28 20:49:45,293] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 20:49:45,294] [INFO] Task started: Prodigal
[2023-06-28 20:49:45,295] [INFO] Running command: gunzip -c /var/lib/cwl/stg6dc66a8d-2b5a-4985-b6ba-da96ae83c164/GCA_017303855.1_ASM1730385v1_genomic.fna.gz | prodigal -d GCA_017303855.1_ASM1730385v1_genomic.fna/cds.fna -a GCA_017303855.1_ASM1730385v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 20:50:07,349] [INFO] Task succeeded: Prodigal
[2023-06-28 20:50:07,350] [INFO] Task started: HMMsearch
[2023-06-28 20:50:07,350] [INFO] Running command: hmmsearch --tblout GCA_017303855.1_ASM1730385v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e9fb72a-8246-4b3a-ae97-9d079573691e/dqc_reference/reference_markers.hmm GCA_017303855.1_ASM1730385v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 20:50:07,667] [INFO] Task succeeded: HMMsearch
[2023-06-28 20:50:07,669] [INFO] Found 6/6 markers.
[2023-06-28 20:50:07,715] [INFO] Query marker FASTA was written to GCA_017303855.1_ASM1730385v1_genomic.fna/markers.fasta
[2023-06-28 20:50:07,715] [INFO] Task started: Blastn
[2023-06-28 20:50:07,716] [INFO] Running command: blastn -query GCA_017303855.1_ASM1730385v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e9fb72a-8246-4b3a-ae97-9d079573691e/dqc_reference/reference_markers.fasta -out GCA_017303855.1_ASM1730385v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:50:08,315] [INFO] Task succeeded: Blastn
[2023-06-28 20:50:08,320] [INFO] Selected 24 target genomes.
[2023-06-28 20:50:08,321] [INFO] Target genome list was writen to GCA_017303855.1_ASM1730385v1_genomic.fna/target_genomes.txt
[2023-06-28 20:50:08,328] [INFO] Task started: fastANI
[2023-06-28 20:50:08,329] [INFO] Running command: fastANI --query /var/lib/cwl/stg6dc66a8d-2b5a-4985-b6ba-da96ae83c164/GCA_017303855.1_ASM1730385v1_genomic.fna.gz --refList GCA_017303855.1_ASM1730385v1_genomic.fna/target_genomes.txt --output GCA_017303855.1_ASM1730385v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 20:50:31,088] [INFO] Task succeeded: fastANI
[2023-06-28 20:50:31,089] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e9fb72a-8246-4b3a-ae97-9d079573691e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 20:50:31,090] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e9fb72a-8246-4b3a-ae97-9d079573691e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 20:50:31,107] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 20:50:31,107] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 20:50:31,108] [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
Niabella beijingensis	strain=3A5MI-3	GCA_020034665.1	2872700	2872700	type	True	76.3622	96	1524	95	below_threshold
Niabella drilacis	strain=DSM 25811	GCA_900101395.1	1285928	1285928	type	True	76.3127	91	1524	95	below_threshold
Flavihumibacter stibioxidans	strain=YS-17	GCA_014332695.1	1834163	1834163	type	True	76.2802	110	1524	95	below_threshold
Niabella aurantiaca	strain=DSM 17617	GCA_000374125.1	379900	379900	type	True	76.2258	86	1524	95	below_threshold
Sediminibacterium goheungense	strain=DSM 28323	GCA_004361915.1	1086393	1086393	type	True	76.2216	84	1524	95	below_threshold
Phnomibacter ginsenosidimutans	strain=SB-02	GCA_009740285.1	2676868	2676868	type	True	76.1384	69	1524	95	below_threshold
Terrimonas ferruginea	strain=DSM 30193	GCA_000425585.1	249	249	type	True	76.1351	153	1524	95	below_threshold
Flavihumibacter fluminis	strain=IMCC34837	GCA_018595675.2	2838157	2838157	type	True	76.1065	90	1524	95	below_threshold
Niabella pedocola	strain=JCM 31011	GCA_021044425.1	1752077	1752077	type	True	76.0976	110	1524	95	below_threshold
Flavihumibacter cheonanensis	strain=WS16	GCA_022352215.1	1442385	1442385	type	True	76.0661	89	1524	95	below_threshold
Niabella ginsenosidivorans	strain=BS26	GCA_001654455.1	1176587	1176587	type	True	75.866	79	1524	95	below_threshold
Paraflavitalea soli	strain=5GH32-13	GCA_003555545.1	2315862	2315862	type	True	75.8635	104	1524	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_002077935.1	354355	354355	type	True	75.7408	98	1524	95	below_threshold
Niastella yeongjuensis	strain=DSM 17621	GCA_900110245.1	354355	354355	type	True	75.6574	96	1524	95	below_threshold
Paraflavitalea devenefica	strain=X16	GCA_011759375.1	2716334	2716334	type	True	75.6521	129	1524	95	below_threshold
Sediminibacterium roseum	strain=SYL130	GCA_009939005.1	1978412	1978412	type	True	75.6229	57	1524	95	below_threshold
Niastella vici	strain=DJ57	GCA_002077945.1	1703345	1703345	type	True	75.6016	107	1524	95	below_threshold
Niastella caeni	strain=HX-16-21	GCA_004834005.1	2569763	2569763	type	True	75.5864	91	1524	95	below_threshold
Foetidibacter luteolus	strain=YG09	GCA_009650435.1	2608880	2608880	type	True	75.268	63	1524	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 20:50:31,111] [INFO] DFAST Taxonomy check result was written to GCA_017303855.1_ASM1730385v1_genomic.fna/tc_result.tsv
[2023-06-28 20:50:31,111] [INFO] ===== Taxonomy check completed =====
[2023-06-28 20:50:31,111] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 20:50:31,112] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e9fb72a-8246-4b3a-ae97-9d079573691e/dqc_reference/checkm_data
[2023-06-28 20:50:31,113] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 20:50:31,162] [INFO] Task started: CheckM
[2023-06-28 20:50:31,162] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017303855.1_ASM1730385v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017303855.1_ASM1730385v1_genomic.fna/checkm_input GCA_017303855.1_ASM1730385v1_genomic.fna/checkm_result
[2023-06-28 20:51:34,409] [INFO] Task succeeded: CheckM
[2023-06-28 20:51:34,411] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 20:51:34,437] [INFO] ===== Completeness check finished =====
[2023-06-28 20:51:34,437] [INFO] ===== Start GTDB Search =====
[2023-06-28 20:51:34,438] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017303855.1_ASM1730385v1_genomic.fna/markers.fasta)
[2023-06-28 20:51:34,438] [INFO] Task started: Blastn
[2023-06-28 20:51:34,438] [INFO] Running command: blastn -query GCA_017303855.1_ASM1730385v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e9fb72a-8246-4b3a-ae97-9d079573691e/dqc_reference/reference_markers_gtdb.fasta -out GCA_017303855.1_ASM1730385v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:51:35,189] [INFO] Task succeeded: Blastn
[2023-06-28 20:51:35,195] [INFO] Selected 17 target genomes.
[2023-06-28 20:51:35,195] [INFO] Target genome list was writen to GCA_017303855.1_ASM1730385v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 20:51:35,248] [INFO] Task started: fastANI
[2023-06-28 20:51:35,248] [INFO] Running command: fastANI --query /var/lib/cwl/stg6dc66a8d-2b5a-4985-b6ba-da96ae83c164/GCA_017303855.1_ASM1730385v1_genomic.fna.gz --refList GCA_017303855.1_ASM1730385v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017303855.1_ASM1730385v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 20:51:48,743] [INFO] Task succeeded: fastANI
[2023-06-28 20:51:48,758] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 20:51:48,758] [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_017303855.1	s__JJ008 sp017303855	100.0	1524	1524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016192105.1	s__JJ008 sp016192105	78.9583	569	1524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016219985.1	s__JJ008 sp016219985	78.9163	587	1524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879565.1	s__JJ008 sp014879565	78.5693	536	1524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016702745.1	s__JJ008 sp016702745	77.4746	337	1524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017303455.1	s__JJ008 sp017303455	77.4379	344	1524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720745.1	s__JJ008 sp016720745	77.4237	367	1524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	98.76	98.76	0.93	0.93	2	-
GCA_016719165.1	s__JJ008 sp016719165	77.3205	340	1524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	97.96	97.46	0.92	0.92	3	-
GCA_002400415.1	s__JJ008 sp002400415	77.0683	321	1524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011331705.1	s__JJ008 sp011331705	77.0226	179	1524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720825.1	s__JJ008 sp016720825	76.8395	273	1524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	98.65	98.65	0.92	0.92	2	-
GCA_002352145.1	s__JJ008 sp002352145	76.8186	230	1524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719815.1	s__JJ008 sp016719815	76.7405	212	1524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	99.30	99.30	0.94	0.94	2	-
GCA_016868455.1	s__JJ008 sp016868455	76.5317	207	1524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JJ008	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014163555.1	s__Flavisolibacter sp014163555	76.0505	89	1524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Flavisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015069695.1	s__JADCRZ01 sp015069695	75.5002	80	1524	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JADCRZ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 20:51:48,760] [INFO] GTDB search result was written to GCA_017303855.1_ASM1730385v1_genomic.fna/result_gtdb.tsv
[2023-06-28 20:51:48,761] [INFO] ===== GTDB Search completed =====
[2023-06-28 20:51:48,766] [INFO] DFAST_QC result json was written to GCA_017303855.1_ASM1730385v1_genomic.fna/dqc_result.json
[2023-06-28 20:51:48,766] [INFO] DFAST_QC completed!
[2023-06-28 20:51:48,766] [INFO] Total running time: 0h2m5s