[2024-01-24 15:02:17,539] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:17,542] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:17,542] [INFO] DQC Reference Directory: /var/lib/cwl/stg53fd029d-9149-402a-985d-4a9321e2b540/dqc_reference
[2024-01-24 15:02:18,937] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:18,938] [INFO] Task started: Prodigal
[2024-01-24 15:02:18,938] [INFO] Running command: gunzip -c /var/lib/cwl/stgfed984c0-e757-48d3-a339-55ad0fff0dff/GCF_008710285.1_ASM871028v1_genomic.fna.gz | prodigal -d GCF_008710285.1_ASM871028v1_genomic.fna/cds.fna -a GCF_008710285.1_ASM871028v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:40,761] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:40,762] [INFO] Task started: HMMsearch
[2024-01-24 15:02:40,762] [INFO] Running command: hmmsearch --tblout GCF_008710285.1_ASM871028v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53fd029d-9149-402a-985d-4a9321e2b540/dqc_reference/reference_markers.hmm GCF_008710285.1_ASM871028v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:41,099] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:41,101] [INFO] Found 6/6 markers.
[2024-01-24 15:02:41,147] [INFO] Query marker FASTA was written to GCF_008710285.1_ASM871028v1_genomic.fna/markers.fasta
[2024-01-24 15:02:41,147] [INFO] Task started: Blastn
[2024-01-24 15:02:41,147] [INFO] Running command: blastn -query GCF_008710285.1_ASM871028v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53fd029d-9149-402a-985d-4a9321e2b540/dqc_reference/reference_markers.fasta -out GCF_008710285.1_ASM871028v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:41,741] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:41,744] [INFO] Selected 22 target genomes.
[2024-01-24 15:02:41,745] [INFO] Target genome list was writen to GCF_008710285.1_ASM871028v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:41,758] [INFO] Task started: fastANI
[2024-01-24 15:02:41,758] [INFO] Running command: fastANI --query /var/lib/cwl/stgfed984c0-e757-48d3-a339-55ad0fff0dff/GCF_008710285.1_ASM871028v1_genomic.fna.gz --refList GCF_008710285.1_ASM871028v1_genomic.fna/target_genomes.txt --output GCF_008710285.1_ASM871028v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:59,584] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:59,585] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53fd029d-9149-402a-985d-4a9321e2b540/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:59,585] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53fd029d-9149-402a-985d-4a9321e2b540/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:59,602] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:02:59,602] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:59,602] [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
Ginsengibacter hankyongi	strain=BR5-29	GCA_008710285.1	2607284	2607284	type	True	100.0	1823	1823	95	conclusive
Hanamia caeni	strain=BO-59	GCA_003721595.1	2294116	2294116	type	True	76.7136	190	1823	95	below_threshold
Ferruginibacter albus	strain=KIS38-8	GCA_020042285.1	2875540	2875540	type	True	76.593	98	1823	95	below_threshold
Lacibacter luteus	strain=TTM-7	GCA_004118265.1	2508719	2508719	type	True	76.0133	65	1823	95	below_threshold
Niabella ginsengisoli	strain=GR10-1	GCA_022513635.1	522298	522298	type	True	75.9805	65	1823	95	below_threshold
Arachidicoccus soli	strain=KIS59-12	GCA_003600625.1	2341117	2341117	type	True	75.9358	50	1823	95	below_threshold
Pinibacter aurantiacus	strain=MAH-26	GCA_019130065.1	2851599	2851599	type	True	75.5973	62	1823	95	below_threshold
Hydrotalea flava	strain=CCUG 51397	GCA_001623405.1	714549	714549	suspected-type	True	75.5408	76	1823	95	below_threshold
Niastella soli	strain=MAH-29	GCA_017742245.1	2821487	2821487	type	True	75.4129	50	1823	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:59,604] [INFO] DFAST Taxonomy check result was written to GCF_008710285.1_ASM871028v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:59,605] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:59,606] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:59,606] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53fd029d-9149-402a-985d-4a9321e2b540/dqc_reference/checkm_data
[2024-01-24 15:02:59,608] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:59,672] [INFO] Task started: CheckM
[2024-01-24 15:02:59,673] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008710285.1_ASM871028v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008710285.1_ASM871028v1_genomic.fna/checkm_input GCF_008710285.1_ASM871028v1_genomic.fna/checkm_result
[2024-01-24 15:04:01,530] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:01,531] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:01,553] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:01,554] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:01,554] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008710285.1_ASM871028v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:01,554] [INFO] Task started: Blastn
[2024-01-24 15:04:01,555] [INFO] Running command: blastn -query GCF_008710285.1_ASM871028v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg53fd029d-9149-402a-985d-4a9321e2b540/dqc_reference/reference_markers_gtdb.fasta -out GCF_008710285.1_ASM871028v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:02,435] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:02,443] [INFO] Selected 21 target genomes.
[2024-01-24 15:04:02,443] [INFO] Target genome list was writen to GCF_008710285.1_ASM871028v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:02,469] [INFO] Task started: fastANI
[2024-01-24 15:04:02,470] [INFO] Running command: fastANI --query /var/lib/cwl/stgfed984c0-e757-48d3-a339-55ad0fff0dff/GCF_008710285.1_ASM871028v1_genomic.fna.gz --refList GCF_008710285.1_ASM871028v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008710285.1_ASM871028v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:16,498] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:16,519] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:16,519] [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_008710285.1	s__Ginsengibacter hankyongi	100.0	1823	1823	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ginsengibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017882215.1	s__Ginsengibacter sp017882215	76.9854	206	1823	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ginsengibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003132765.1	s__Ginsengibacter sp003132765	76.9738	256	1823	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ginsengibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003721595.1	s__Ginsengibacter sp003721595	76.7375	188	1823	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ginsengibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002050465.1	s__Ginsengibacter sp002050465	76.6559	114	1823	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ginsengibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016710595.1	s__Ferruginibacter sp016710595	76.5532	72	1823	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016721385.1	s__Ferruginibacter sp016721385	76.5338	72	1823	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268075.1	s__Ginsengibacter sp018268075	76.3939	132	1823	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ginsengibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016703625.1	s__Ferruginibacter sp016703625	76.2259	81	1823	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	97.77	96.12	0.94	0.91	5	-
GCA_017983695.1	s__Ferruginibacter sp017983695	76.0829	134	1823	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013694745.1	s__Ginsengibacter sp013694745	76.0699	131	1823	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ginsengibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013141115.1	s__Ferruginibacter sp013141115	75.9861	133	1823	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013286305.1	s__JABDFW01 sp013286305	75.961	57	1823	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__JABDFW01	95.0	99.29	99.29	0.63	0.63	2	-
GCA_017882205.1	s__Ginsengibacter sp017882205	75.9333	72	1823	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ginsengibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016200915.1	s__AWTP1-9 sp016200915	75.8411	100	1823	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__AWTP1-9	95.0	99.92	99.92	0.98	0.98	2	-
GCA_018268155.1	s__Ferruginibacter sp018268155	75.8351	104	1823	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903878475.1	s__Ferruginibacter sp903878475	75.6689	50	1823	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	98.41	98.13	0.86	0.85	5	-
GCA_001623405.1	s__Hydrotalea flava	75.5673	74	1823	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Hydrotalea	95.0	95.88	95.18	0.90	0.86	13	-
GCA_018057635.1	s__Ferruginibacter sp018057635	75.4096	58	1823	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903837525.1	s__Ferruginibacter sp903837525	75.244	62	1823	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Ferruginibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:16,521] [INFO] GTDB search result was written to GCF_008710285.1_ASM871028v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:16,521] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:16,525] [INFO] DFAST_QC result json was written to GCF_008710285.1_ASM871028v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:16,525] [INFO] DFAST_QC completed!
[2024-01-24 15:04:16,526] [INFO] Total running time: 0h1m59s