[2023-06-30 17:00:37,336] [INFO] DFAST_QC pipeline started.
[2023-06-30 17:00:37,338] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 17:00:37,338] [INFO] DQC Reference Directory: /var/lib/cwl/stge50fce26-929c-4c50-9338-49e443ebac14/dqc_reference
[2023-06-30 17:00:38,512] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 17:00:38,513] [INFO] Task started: Prodigal
[2023-06-30 17:00:38,513] [INFO] Running command: gunzip -c /var/lib/cwl/stgd49f4357-5e18-4575-b1a6-e7d17f192648/GCA_016183765.1_ASM1618376v1_genomic.fna.gz | prodigal -d GCA_016183765.1_ASM1618376v1_genomic.fna/cds.fna -a GCA_016183765.1_ASM1618376v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 17:00:57,913] [INFO] Task succeeded: Prodigal
[2023-06-30 17:00:57,914] [INFO] Task started: HMMsearch
[2023-06-30 17:00:57,914] [INFO] Running command: hmmsearch --tblout GCA_016183765.1_ASM1618376v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge50fce26-929c-4c50-9338-49e443ebac14/dqc_reference/reference_markers.hmm GCA_016183765.1_ASM1618376v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 17:00:58,192] [INFO] Task succeeded: HMMsearch
[2023-06-30 17:00:58,193] [INFO] Found 6/6 markers.
[2023-06-30 17:00:58,226] [INFO] Query marker FASTA was written to GCA_016183765.1_ASM1618376v1_genomic.fna/markers.fasta
[2023-06-30 17:00:58,227] [INFO] Task started: Blastn
[2023-06-30 17:00:58,227] [INFO] Running command: blastn -query GCA_016183765.1_ASM1618376v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge50fce26-929c-4c50-9338-49e443ebac14/dqc_reference/reference_markers.fasta -out GCA_016183765.1_ASM1618376v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 17:00:58,813] [INFO] Task succeeded: Blastn
[2023-06-30 17:00:58,818] [INFO] Selected 17 target genomes.
[2023-06-30 17:00:58,819] [INFO] Target genome list was writen to GCA_016183765.1_ASM1618376v1_genomic.fna/target_genomes.txt
[2023-06-30 17:00:58,835] [INFO] Task started: fastANI
[2023-06-30 17:00:58,836] [INFO] Running command: fastANI --query /var/lib/cwl/stgd49f4357-5e18-4575-b1a6-e7d17f192648/GCA_016183765.1_ASM1618376v1_genomic.fna.gz --refList GCA_016183765.1_ASM1618376v1_genomic.fna/target_genomes.txt --output GCA_016183765.1_ASM1618376v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 17:01:12,383] [INFO] Task succeeded: fastANI
[2023-06-30 17:01:12,383] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge50fce26-929c-4c50-9338-49e443ebac14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 17:01:12,384] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge50fce26-929c-4c50-9338-49e443ebac14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 17:01:12,401] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 17:01:12,401] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 17:01:12,401] [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
Sediminibacterium roseum	strain=SYL130	GCA_009939005.1	1978412	1978412	type	True	78.0579	361	1214	95	below_threshold
Sediminibacterium soli	strain=WSJ-3	GCA_009939225.1	2698829	2698829	type	True	77.7846	373	1214	95	below_threshold
Sediminibacterium ginsengisoli	strain=DSM 22335	GCA_900167075.1	413434	413434	type	True	77.6335	296	1214	95	below_threshold
Sediminibacterium goheungense	strain=DSM 28323	GCA_004361915.1	1086393	1086393	type	True	77.355	231	1214	95	below_threshold
Filimonas zeae	strain=CGMCC 1.15290	GCA_014641615.1	1737353	1737353	type	True	76.5372	102	1214	95	below_threshold
Filimonas effusa	strain=TTM-71	GCA_004118675.1	2508721	2508721	type	True	76.5188	99	1214	95	below_threshold
Deminuibacter soli	strain=K23C18032701	GCA_003412455.1	2291815	2291815	type	True	76.4806	153	1214	95	below_threshold
Flavihumibacter stibioxidans	strain=YS-17	GCA_014332695.1	1834163	1834163	type	True	76.4196	114	1214	95	below_threshold
Panacibacter microcysteis	strain=DH6	GCA_015831355.1	2793269	2793269	type	True	76.1658	97	1214	95	below_threshold
Flavihumibacter rivuli	strain=IMCC34838	GCA_018595685.2	2838156	2838156	type	True	76.1543	111	1214	95	below_threshold
Niabella pedocola	strain=JCM 31011	GCA_021044425.1	1752077	1752077	type	True	76.1249	68	1214	95	below_threshold
Niabella beijingensis	strain=3A5MI-3	GCA_020034665.1	2872700	2872700	type	True	75.9924	80	1214	95	below_threshold
Foetidibacter luteolus	strain=YG09	GCA_009650435.1	2608880	2608880	type	True	75.9687	81	1214	95	below_threshold
Phnomibacter ginsenosidimutans	strain=SB-02	GCA_009740285.1	2676868	2676868	type	True	75.965	74	1214	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 17:01:12,403] [INFO] DFAST Taxonomy check result was written to GCA_016183765.1_ASM1618376v1_genomic.fna/tc_result.tsv
[2023-06-30 17:01:12,404] [INFO] ===== Taxonomy check completed =====
[2023-06-30 17:01:12,404] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 17:01:12,404] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge50fce26-929c-4c50-9338-49e443ebac14/dqc_reference/checkm_data
[2023-06-30 17:01:12,405] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 17:01:12,442] [INFO] Task started: CheckM
[2023-06-30 17:01:12,442] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016183765.1_ASM1618376v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016183765.1_ASM1618376v1_genomic.fna/checkm_input GCA_016183765.1_ASM1618376v1_genomic.fna/checkm_result
[2023-06-30 17:02:08,760] [INFO] Task succeeded: CheckM
[2023-06-30 17:02:08,761] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 17:02:08,784] [INFO] ===== Completeness check finished =====
[2023-06-30 17:02:08,784] [INFO] ===== Start GTDB Search =====
[2023-06-30 17:02:08,785] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016183765.1_ASM1618376v1_genomic.fna/markers.fasta)
[2023-06-30 17:02:08,785] [INFO] Task started: Blastn
[2023-06-30 17:02:08,785] [INFO] Running command: blastn -query GCA_016183765.1_ASM1618376v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge50fce26-929c-4c50-9338-49e443ebac14/dqc_reference/reference_markers_gtdb.fasta -out GCA_016183765.1_ASM1618376v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 17:02:09,579] [INFO] Task succeeded: Blastn
[2023-06-30 17:02:09,584] [INFO] Selected 15 target genomes.
[2023-06-30 17:02:09,585] [INFO] Target genome list was writen to GCA_016183765.1_ASM1618376v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 17:02:09,587] [INFO] Task started: fastANI
[2023-06-30 17:02:09,587] [INFO] Running command: fastANI --query /var/lib/cwl/stgd49f4357-5e18-4575-b1a6-e7d17f192648/GCA_016183765.1_ASM1618376v1_genomic.fna.gz --refList GCA_016183765.1_ASM1618376v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016183765.1_ASM1618376v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 17:02:19,514] [INFO] Task succeeded: fastANI
[2023-06-30 17:02:19,531] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 17:02:19,532] [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_016183765.1	s__Sediminibacterium sp016183765	100.0	1212	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004297075.1	s__Sediminibacterium sp004297075	80.3678	590	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	98.05	98.05	0.89	0.89	2	-
GCF_009939005.1	s__Sediminibacterium roseum	78.0579	361	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004028765.1	s__Sediminibacterium sp004028765	77.9466	453	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009939225.1	s__Sediminibacterium soli	77.8018	371	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019247775.1	s__Sediminibacterium sp019247775	77.7253	334	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167075.1	s__Sediminibacterium ginsengisoli	77.6332	296	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903913355.1	s__Sediminibacterium sp903913355	77.5792	194	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000515315.1	s__Sediminibacterium sp000515315	77.5363	281	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	96.66	96.66	0.84	0.84	2	-
GCA_013289065.1	s__Sediminibacterium sp013289065	77.482	207	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002973575.1	s__Sediminibacterium magnilacihabitans	77.4194	278	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	99.08	98.17	0.92	0.85	3	-
GCA_903926855.1	s__Sediminibacterium sp903926855	76.9918	219	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	98.86	97.42	0.87	0.81	7	-
GCF_015831355.1	s__Panacibacter sp015831355	76.1658	97	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Panacibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200915.1	s__AWTP1-9 sp016200915	75.6484	57	1214	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__AWTP1-9	95.0	99.92	99.92	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2023-06-30 17:02:19,534] [INFO] GTDB search result was written to GCA_016183765.1_ASM1618376v1_genomic.fna/result_gtdb.tsv
[2023-06-30 17:02:19,535] [INFO] ===== GTDB Search completed =====
[2023-06-30 17:02:19,539] [INFO] DFAST_QC result json was written to GCA_016183765.1_ASM1618376v1_genomic.fna/dqc_result.json
[2023-06-30 17:02:19,539] [INFO] DFAST_QC completed!
[2023-06-30 17:02:19,539] [INFO] Total running time: 0h1m42s