[2024-01-24 13:12:54,710] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:54,713] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:54,713] [INFO] DQC Reference Directory: /var/lib/cwl/stgf563be59-fafe-414a-b82c-fd928514b0f2/dqc_reference
[2024-01-24 13:12:56,041] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:56,042] [INFO] Task started: Prodigal
[2024-01-24 13:12:56,042] [INFO] Running command: gunzip -c /var/lib/cwl/stg003abc43-5098-47ff-92bc-221352fbf496/GCF_002148965.1_ASM214896v1_genomic.fna.gz | prodigal -d GCF_002148965.1_ASM214896v1_genomic.fna/cds.fna -a GCF_002148965.1_ASM214896v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:19,747] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:19,747] [INFO] Task started: HMMsearch
[2024-01-24 13:13:19,747] [INFO] Running command: hmmsearch --tblout GCF_002148965.1_ASM214896v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf563be59-fafe-414a-b82c-fd928514b0f2/dqc_reference/reference_markers.hmm GCF_002148965.1_ASM214896v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:20,174] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:20,176] [INFO] Found 6/6 markers.
[2024-01-24 13:13:20,245] [INFO] Query marker FASTA was written to GCF_002148965.1_ASM214896v1_genomic.fna/markers.fasta
[2024-01-24 13:13:20,245] [INFO] Task started: Blastn
[2024-01-24 13:13:20,246] [INFO] Running command: blastn -query GCF_002148965.1_ASM214896v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf563be59-fafe-414a-b82c-fd928514b0f2/dqc_reference/reference_markers.fasta -out GCF_002148965.1_ASM214896v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:21,584] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:21,588] [INFO] Selected 14 target genomes.
[2024-01-24 13:13:21,589] [INFO] Target genome list was writen to GCF_002148965.1_ASM214896v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:21,595] [INFO] Task started: fastANI
[2024-01-24 13:13:21,596] [INFO] Running command: fastANI --query /var/lib/cwl/stg003abc43-5098-47ff-92bc-221352fbf496/GCF_002148965.1_ASM214896v1_genomic.fna.gz --refList GCF_002148965.1_ASM214896v1_genomic.fna/target_genomes.txt --output GCF_002148965.1_ASM214896v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:51,986] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:51,987] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf563be59-fafe-414a-b82c-fd928514b0f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:51,988] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf563be59-fafe-414a-b82c-fd928514b0f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:52,001] [INFO] Found 14 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:13:52,001] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:13:52,001] [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
Streptomyces swartbergensis	strain=HMC13	GCA_002148965.1	487165	487165	type	True	100.0	2616	2650	95	inconclusive
Streptomyces coeruleorubidus	strain=JCM 4359	GCA_014649455.1	116188	116188	suspected-type	True	95.045	2142	2650	95	inconclusive
Streptomyces coeruleorubidus	strain=ATCC 13740	GCA_008705135.1	116188	116188	suspected-type	True	95.0055	2149	2650	95	inconclusive
Streptomyces azureus	strain=ATCC 14921	GCA_001270025.1	146537	146537	type	True	94.9559	2006	2650	95	below_threshold
Streptomyces caelestis	strain=JCM 4566	GCA_014650295.1	36816	36816	type	True	94.2834	2036	2650	95	below_threshold
Streptomyces caelestis	strain=DSM 40084	GCA_014205255.1	36816	36816	type	True	94.2008	2056	2650	95	below_threshold
Streptomyces africanus	strain=NRRL B-24243	GCA_002150735.1	231024	231024	type	True	93.2262	1852	2650	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	91.7263	2025	2650	95	below_threshold
Streptomyces purpurascens	strain=DSM 40310	GCA_021390235.1	1924	1924	type	True	91.3804	2004	2650	95	below_threshold
Streptomyces hawaiiensis	strain=ATCC 12236	GCA_004803895.1	67305	67305	type	True	90.8036	2003	2650	95	below_threshold
Streptomyces djakartensis	strain=JCM 4957	GCA_014651075.1	68193	68193	type	True	90.3503	1789	2650	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	90.2888	1683	2650	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	90.0304	1703	2650	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	85.5304	1558	2650	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:52,003] [INFO] DFAST Taxonomy check result was written to GCF_002148965.1_ASM214896v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:52,003] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:52,003] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:52,004] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf563be59-fafe-414a-b82c-fd928514b0f2/dqc_reference/checkm_data
[2024-01-24 13:13:52,004] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:52,088] [INFO] Task started: CheckM
[2024-01-24 13:13:52,089] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002148965.1_ASM214896v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002148965.1_ASM214896v1_genomic.fna/checkm_input GCF_002148965.1_ASM214896v1_genomic.fna/checkm_result
[2024-01-24 13:15:03,509] [INFO] Task succeeded: CheckM
[2024-01-24 13:15:03,510] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 13:15:03,529] [INFO] ===== Completeness check finished =====
[2024-01-24 13:15:03,529] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:15:03,530] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002148965.1_ASM214896v1_genomic.fna/markers.fasta)
[2024-01-24 13:15:03,530] [INFO] Task started: Blastn
[2024-01-24 13:15:03,530] [INFO] Running command: blastn -query GCF_002148965.1_ASM214896v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf563be59-fafe-414a-b82c-fd928514b0f2/dqc_reference/reference_markers_gtdb.fasta -out GCF_002148965.1_ASM214896v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:15:05,782] [INFO] Task succeeded: Blastn
[2024-01-24 13:15:05,785] [INFO] Selected 8 target genomes.
[2024-01-24 13:15:05,785] [INFO] Target genome list was writen to GCF_002148965.1_ASM214896v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:15:05,797] [INFO] Task started: fastANI
[2024-01-24 13:15:05,798] [INFO] Running command: fastANI --query /var/lib/cwl/stg003abc43-5098-47ff-92bc-221352fbf496/GCF_002148965.1_ASM214896v1_genomic.fna.gz --refList GCF_002148965.1_ASM214896v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002148965.1_ASM214896v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:25,990] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:26,004] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:26,004] [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_002148965.1	s__Streptomyces swartbergensis	100.0	2616	2650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008705135.1	s__Streptomyces coeruleorubidus	94.9973	2150	2650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.68	95.03	0.91	0.83	4	-
GCF_014205255.1	s__Streptomyces caelestis	94.1973	2057	2650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000415505.1	s__Streptomyces afghaniensis	93.7789	1948	2650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900236475.1	s__Streptomyces chartreusis_D	93.5491	2054	2650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.99	99.98	1.00	1.00	4	-
GCF_002150735.1	s__Streptomyces africanus	93.2037	1853	2650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717875.1	s__Streptomyces sp000717875	90.7984	1856	2650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.70	99.70	0.96	0.96	2	-
GCF_004803895.1	s__Streptomyces hawaiiensis	90.7905	2005	2650	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.39	95.39	0.84	0.84	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:15:26,006] [INFO] GTDB search result was written to GCF_002148965.1_ASM214896v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:26,007] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:26,010] [INFO] DFAST_QC result json was written to GCF_002148965.1_ASM214896v1_genomic.fna/dqc_result.json
[2024-01-24 13:15:26,010] [INFO] DFAST_QC completed!
[2024-01-24 13:15:26,011] [INFO] Total running time: 0h2m31s