[2024-01-24 12:22:33,816] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:33,818] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:33,818] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4b2d565-4276-471b-ace9-73fe861a7c2f/dqc_reference
[2024-01-24 12:22:35,261] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:35,262] [INFO] Task started: Prodigal
[2024-01-24 12:22:35,263] [INFO] Running command: gunzip -c /var/lib/cwl/stgf37355e6-fbe9-4ec0-ab25-7e16ecb7cc6e/GCF_002155895.1_ASM215589v1_genomic.fna.gz | prodigal -d GCF_002155895.1_ASM215589v1_genomic.fna/cds.fna -a GCF_002155895.1_ASM215589v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:55,039] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:55,040] [INFO] Task started: HMMsearch
[2024-01-24 12:22:55,040] [INFO] Running command: hmmsearch --tblout GCF_002155895.1_ASM215589v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4b2d565-4276-471b-ace9-73fe861a7c2f/dqc_reference/reference_markers.hmm GCF_002155895.1_ASM215589v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:55,416] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:55,417] [INFO] Found 6/6 markers.
[2024-01-24 12:22:55,480] [INFO] Query marker FASTA was written to GCF_002155895.1_ASM215589v1_genomic.fna/markers.fasta
[2024-01-24 12:22:55,480] [INFO] Task started: Blastn
[2024-01-24 12:22:55,481] [INFO] Running command: blastn -query GCF_002155895.1_ASM215589v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4b2d565-4276-471b-ace9-73fe861a7c2f/dqc_reference/reference_markers.fasta -out GCF_002155895.1_ASM215589v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:56,865] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:56,869] [INFO] Selected 21 target genomes.
[2024-01-24 12:22:56,870] [INFO] Target genome list was writen to GCF_002155895.1_ASM215589v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:56,878] [INFO] Task started: fastANI
[2024-01-24 12:22:56,878] [INFO] Running command: fastANI --query /var/lib/cwl/stgf37355e6-fbe9-4ec0-ab25-7e16ecb7cc6e/GCF_002155895.1_ASM215589v1_genomic.fna.gz --refList GCF_002155895.1_ASM215589v1_genomic.fna/target_genomes.txt --output GCF_002155895.1_ASM215589v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:36,953] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:36,954] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4b2d565-4276-471b-ace9-73fe861a7c2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:36,954] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4b2d565-4276-471b-ace9-73fe861a7c2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:36,976] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:23:36,976] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:23:36,976] [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 mutabilis	strain=JCM 4400	GCA_014649815.1	67332	67332	type	True	91.9064	1725	2204	95	below_threshold
Streptomyces ambofaciens	strain=ATCC 23877	GCA_001267885.1	1889	1889	type	True	89.8734	1772	2204	95	below_threshold
Streptomyces rubrogriseus	strain=NBRC 15455	GCA_003112595.1	194673	194673	type	True	89.7031	1727	2204	95	below_threshold
Streptomyces hyderabadensis	strain=JCM 17657	GCA_020404845.1	598549	598549	type	True	89.6738	1681	2204	95	below_threshold
Streptomyces tendae	strain=JCM 4610	GCA_014650435.1	1932	1932	type	True	89.5427	1722	2204	95	below_threshold
Streptomyces anthocyanicus	strain=JCM 5058	GCA_014651155.1	68174	68174	type	True	89.5389	1748	2204	95	below_threshold
Streptomyces violaceorubidus	strain=NRRL B-16381	GCA_000717995.1	284042	284042	type	True	89.4135	1619	2204	95	below_threshold
Streptomyces ardesiacus	strain=NBRC 15402	GCA_003112575.1	285564	285564	type	True	89.1826	1669	2204	95	below_threshold
Streptomyces solaniscabiei	strain=FS70	GCA_020312315.1	2683255	2683255	type	True	89.1144	1644	2204	95	below_threshold
Streptomyces flaveolus	strain=JCM 4032	GCA_014648815.1	67297	67297	type	True	89.0416	1655	2204	95	below_threshold
Streptomyces parvulus	strain=JCM 4068	GCA_014648855.1	146923	146923	type	True	88.891	1668	2204	95	below_threshold
Streptomyces olivaceus	strain=NRRL B-3009	GCA_000721235.1	47716	47716	type	True	88.5948	1629	2204	95	below_threshold
Streptomyces olivaceus	strain=NRRL B-3009	GCA_015645455.1	47716	47716	type	True	88.5931	1603	2204	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	88.2296	1660	2204	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	86.3967	1398	2204	95	below_threshold
Streptomyces daghestanicus	strain=NBRC 12762	GCA_020521275.1	66885	66885	suspected-type	True	86.2932	1559	2204	95	below_threshold
Streptomyces daghestanicus	strain=JCM 4365	GCA_014649475.1	66885	66885	suspected-type	True	86.266	1532	2204	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	85.9166	1519	2204	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	85.6134	1403	2204	95	below_threshold
Streptomyces djakartensis	strain=JCM 4957	GCA_014651075.1	68193	68193	type	True	85.5139	1393	2204	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	85.1505	1342	2204	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:36,978] [INFO] DFAST Taxonomy check result was written to GCF_002155895.1_ASM215589v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:36,979] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:36,979] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:36,980] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4b2d565-4276-471b-ace9-73fe861a7c2f/dqc_reference/checkm_data
[2024-01-24 12:23:36,980] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:37,051] [INFO] Task started: CheckM
[2024-01-24 12:23:37,051] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002155895.1_ASM215589v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002155895.1_ASM215589v1_genomic.fna/checkm_input GCF_002155895.1_ASM215589v1_genomic.fna/checkm_result
[2024-01-24 12:25:02,263] [INFO] Task succeeded: CheckM
[2024-01-24 12:25:02,265] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.42%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-24 12:25:02,301] [INFO] ===== Completeness check finished =====
[2024-01-24 12:25:02,301] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:25:02,302] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002155895.1_ASM215589v1_genomic.fna/markers.fasta)
[2024-01-24 12:25:02,302] [INFO] Task started: Blastn
[2024-01-24 12:25:02,302] [INFO] Running command: blastn -query GCF_002155895.1_ASM215589v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4b2d565-4276-471b-ace9-73fe861a7c2f/dqc_reference/reference_markers_gtdb.fasta -out GCF_002155895.1_ASM215589v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:04,384] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:04,388] [INFO] Selected 14 target genomes.
[2024-01-24 12:25:04,389] [INFO] Target genome list was writen to GCF_002155895.1_ASM215589v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:25:04,400] [INFO] Task started: fastANI
[2024-01-24 12:25:04,400] [INFO] Running command: fastANI --query /var/lib/cwl/stgf37355e6-fbe9-4ec0-ab25-7e16ecb7cc6e/GCF_002155895.1_ASM215589v1_genomic.fna.gz --refList GCF_002155895.1_ASM215589v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002155895.1_ASM215589v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:25:31,742] [INFO] Task succeeded: fastANI
[2024-01-24 12:25:31,760] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:25:31,761] [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_002155895.1	s__Streptomyces rochei	100.0	2185	2204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.80	98.25	0.91	0.79	28	conclusive
GCF_001905385.1	s__Streptomyces sp001905385	92.5814	1753	2204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.01	96.01	0.83	0.83	2	-
GCF_014649815.1	s__Streptomyces mutabilis	91.8994	1725	2204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.69	95.91	0.82	0.76	4	-
GCF_002005225.1	s__Streptomyces pactum_A	90.0228	1748	2204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.98	0.98	2	-
GCF_003112595.1	s__Streptomyces rubrogriseus	89.7034	1727	2204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.9168	N/A	N/A	N/A	N/A	1	-
GCF_000772045.1	s__Streptomyces sp000772045	89.635	1717	2204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.88	95.78	0.85	0.82	9	-
GCF_002939385.1	s__Streptomyces sp002939385	89.5721	1672	2204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.14	95.04	0.81	0.78	6	-
GCF_000717995.1	s__Streptomyces violaceorubidus	89.4089	1619	2204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003112555.1	s__Streptomyces coelicoflavus	89.3847	1742	2204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.84	97.03	0.90	0.86	6	-
GCF_003112575.1	s__Streptomyces ardesiacus	89.1674	1669	2204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.97	95.84	0.93	0.82	10	-
GCF_014648855.1	s__Streptomyces parvulus	88.88	1669	2204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.39	95.93	0.93	0.87	4	-
GCF_002005565.1	s__Streptomyces sp002005565	88.8204	1553	2204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018982965.1	s__Streptomyces sp018982965	88.698	1560	2204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018614415.1	s__Streptomyces sp018614415	86.6599	1509	2204	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:25:31,762] [INFO] GTDB search result was written to GCF_002155895.1_ASM215589v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:25:31,763] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:25:31,768] [INFO] DFAST_QC result json was written to GCF_002155895.1_ASM215589v1_genomic.fna/dqc_result.json
[2024-01-24 12:25:31,768] [INFO] DFAST_QC completed!
[2024-01-24 12:25:31,768] [INFO] Total running time: 0h2m58s