[2024-01-25 19:02:20,496] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:02:20,501] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:02:20,501] [INFO] DQC Reference Directory: /var/lib/cwl/stgc45d3d8c-b9ac-4a51-93ec-1297a8acc09d/dqc_reference
[2024-01-25 19:02:21,621] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:02:21,621] [INFO] Task started: Prodigal
[2024-01-25 19:02:21,622] [INFO] Running command: gunzip -c /var/lib/cwl/stg1682bd04-e2b4-4a25-9c13-e9c8ec3939b8/GCF_014174495.1_ASM1417449v1_genomic.fna.gz | prodigal -d GCF_014174495.1_ASM1417449v1_genomic.fna/cds.fna -a GCF_014174495.1_ASM1417449v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:02:44,855] [INFO] Task succeeded: Prodigal
[2024-01-25 19:02:44,855] [INFO] Task started: HMMsearch
[2024-01-25 19:02:44,855] [INFO] Running command: hmmsearch --tblout GCF_014174495.1_ASM1417449v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc45d3d8c-b9ac-4a51-93ec-1297a8acc09d/dqc_reference/reference_markers.hmm GCF_014174495.1_ASM1417449v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:02:45,230] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:02:45,231] [INFO] Found 6/6 markers.
[2024-01-25 19:02:45,302] [INFO] Query marker FASTA was written to GCF_014174495.1_ASM1417449v1_genomic.fna/markers.fasta
[2024-01-25 19:02:45,303] [INFO] Task started: Blastn
[2024-01-25 19:02:45,303] [INFO] Running command: blastn -query GCF_014174495.1_ASM1417449v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc45d3d8c-b9ac-4a51-93ec-1297a8acc09d/dqc_reference/reference_markers.fasta -out GCF_014174495.1_ASM1417449v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:02:46,561] [INFO] Task succeeded: Blastn
[2024-01-25 19:02:46,563] [INFO] Selected 12 target genomes.
[2024-01-25 19:02:46,564] [INFO] Target genome list was writen to GCF_014174495.1_ASM1417449v1_genomic.fna/target_genomes.txt
[2024-01-25 19:02:46,576] [INFO] Task started: fastANI
[2024-01-25 19:02:46,576] [INFO] Running command: fastANI --query /var/lib/cwl/stg1682bd04-e2b4-4a25-9c13-e9c8ec3939b8/GCF_014174495.1_ASM1417449v1_genomic.fna.gz --refList GCF_014174495.1_ASM1417449v1_genomic.fna/target_genomes.txt --output GCF_014174495.1_ASM1417449v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:03:11,279] [INFO] Task succeeded: fastANI
[2024-01-25 19:03:11,280] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc45d3d8c-b9ac-4a51-93ec-1297a8acc09d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:03:11,280] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc45d3d8c-b9ac-4a51-93ec-1297a8acc09d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:03:11,290] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:03:11,290] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:03:11,290] [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
Amycolatopsis nivea	strain=CFH S0261	GCA_004522235.1	1644109	1644109	type	True	92.3142	2246	3084	95	below_threshold
Amycolatopsis dendrobii	strain=DR6-1	GCA_014145675.1	2760662	2760662	type	True	92.2798	2304	3084	95	below_threshold
Amycolatopsis rubida	strain=DSM 44637	GCA_900115345.1	112413	112413	type	True	91.8459	2210	3084	95	below_threshold
Amycolatopsis circi	strain=DSM 45561	GCA_003385235.1	871959	871959	type	True	91.8109	2150	3084	95	below_threshold
Amycolatopsis benzoatilytica	strain=AK 16/65	GCA_000383915.1	346045	346045	type	True	86.8828	2012	3084	95	below_threshold
Amycolatopsis sulphurea	strain=DSM 46092	GCA_002564045.1	76022	76022	type	True	83.1185	1362	3084	95	below_threshold
Amycolatopsis panacis	strain=YIM PH21725	GCA_003600245.1	2340917	2340917	type	True	82.9921	1329	3084	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	81.4361	1558	3084	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	79.9161	1155	3084	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	79.0277	965	3084	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	78.076	783	3084	95	below_threshold
Lentzea aerocolonigenes	strain=DSM 40034	GCA_024171805.1	68170	68170	type	True	77.7599	866	3084	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:03:11,291] [INFO] DFAST Taxonomy check result was written to GCF_014174495.1_ASM1417449v1_genomic.fna/tc_result.tsv
[2024-01-25 19:03:11,292] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:03:11,292] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:03:11,292] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc45d3d8c-b9ac-4a51-93ec-1297a8acc09d/dqc_reference/checkm_data
[2024-01-25 19:03:11,293] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:03:11,380] [INFO] Task started: CheckM
[2024-01-25 19:03:11,380] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014174495.1_ASM1417449v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014174495.1_ASM1417449v1_genomic.fna/checkm_input GCF_014174495.1_ASM1417449v1_genomic.fna/checkm_result
[2024-01-25 19:04:28,647] [INFO] Task succeeded: CheckM
[2024-01-25 19:04:28,648] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:04:28,671] [INFO] ===== Completeness check finished =====
[2024-01-25 19:04:28,672] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:04:28,672] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014174495.1_ASM1417449v1_genomic.fna/markers.fasta)
[2024-01-25 19:04:28,673] [INFO] Task started: Blastn
[2024-01-25 19:04:28,673] [INFO] Running command: blastn -query GCF_014174495.1_ASM1417449v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc45d3d8c-b9ac-4a51-93ec-1297a8acc09d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014174495.1_ASM1417449v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:30,698] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:30,701] [INFO] Selected 7 target genomes.
[2024-01-25 19:04:30,701] [INFO] Target genome list was writen to GCF_014174495.1_ASM1417449v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:04:30,710] [INFO] Task started: fastANI
[2024-01-25 19:04:30,710] [INFO] Running command: fastANI --query /var/lib/cwl/stg1682bd04-e2b4-4a25-9c13-e9c8ec3939b8/GCF_014174495.1_ASM1417449v1_genomic.fna.gz --refList GCF_014174495.1_ASM1417449v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014174495.1_ASM1417449v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:04:48,731] [INFO] Task succeeded: fastANI
[2024-01-25 19:04:48,737] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:04:48,737] [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_014174495.1	s__Amycolatopsis echigonensis	100.0	3074	3084	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	98.67	98.67	0.88	0.88	2	conclusive
GCF_000411975.1	s__Amycolatopsis orientalis_D	92.5791	2345	3084	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004522235.1	s__Amycolatopsis nivea	92.338	2243	3084	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	97.97	97.28	0.91	0.88	6	-
GCF_014145675.1	s__Amycolatopsis sp014145675	92.2591	2307	3084	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002796545.1	s__Amycolatopsis sp002796545	92.2588	2231	3084	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.98	99.98	1.00	1.00	2	-
GCF_900115345.1	s__Amycolatopsis rubida	91.8702	2207	3084	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.28	99.27	0.88	0.87	4	-
GCF_003385235.1	s__Amycolatopsis circi	91.817	2148	3084	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:04:48,739] [INFO] GTDB search result was written to GCF_014174495.1_ASM1417449v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:04:48,739] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:04:48,742] [INFO] DFAST_QC result json was written to GCF_014174495.1_ASM1417449v1_genomic.fna/dqc_result.json
[2024-01-25 19:04:48,742] [INFO] DFAST_QC completed!
[2024-01-25 19:04:48,742] [INFO] Total running time: 0h2m28s