[2024-01-24 10:57:38,914] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:38,916] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:38,916] [INFO] DQC Reference Directory: /var/lib/cwl/stge0bd3e15-2da7-47d3-bf87-2adb3dcb1a67/dqc_reference
[2024-01-24 10:57:40,303] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:40,304] [INFO] Task started: Prodigal
[2024-01-24 10:57:40,304] [INFO] Running command: gunzip -c /var/lib/cwl/stge49b80e9-a571-4be8-8116-061f0a0358f8/GCF_001418335.1_ASM141833v1_genomic.fna.gz | prodigal -d GCF_001418335.1_ASM141833v1_genomic.fna/cds.fna -a GCF_001418335.1_ASM141833v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:04,268] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:04,269] [INFO] Task started: HMMsearch
[2024-01-24 10:58:04,269] [INFO] Running command: hmmsearch --tblout GCF_001418335.1_ASM141833v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0bd3e15-2da7-47d3-bf87-2adb3dcb1a67/dqc_reference/reference_markers.hmm GCF_001418335.1_ASM141833v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:04,650] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:04,652] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge49b80e9-a571-4be8-8116-061f0a0358f8/GCF_001418335.1_ASM141833v1_genomic.fna.gz]
[2024-01-24 10:58:04,722] [INFO] Query marker FASTA was written to GCF_001418335.1_ASM141833v1_genomic.fna/markers.fasta
[2024-01-24 10:58:04,723] [INFO] Task started: Blastn
[2024-01-24 10:58:04,723] [INFO] Running command: blastn -query GCF_001418335.1_ASM141833v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0bd3e15-2da7-47d3-bf87-2adb3dcb1a67/dqc_reference/reference_markers.fasta -out GCF_001418335.1_ASM141833v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:05,976] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:05,980] [INFO] Selected 25 target genomes.
[2024-01-24 10:58:05,981] [INFO] Target genome list was writen to GCF_001418335.1_ASM141833v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:06,007] [INFO] Task started: fastANI
[2024-01-24 10:58:06,007] [INFO] Running command: fastANI --query /var/lib/cwl/stge49b80e9-a571-4be8-8116-061f0a0358f8/GCF_001418335.1_ASM141833v1_genomic.fna.gz --refList GCF_001418335.1_ASM141833v1_genomic.fna/target_genomes.txt --output GCF_001418335.1_ASM141833v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:57,715] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:57,716] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0bd3e15-2da7-47d3-bf87-2adb3dcb1a67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:57,716] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0bd3e15-2da7-47d3-bf87-2adb3dcb1a67/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:57,735] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:57,735] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:57,735] [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 aurantiacus	strain=NRRL ISP-5412	GCA_001418335.1	47760	47760	type	True	100.0	2783	2811	95	conclusive
Streptomyces phaeochromogenes	strain=NRRL B-1248	GCA_001418655.1	1923	1923	type	True	88.0723	1777	2811	95	below_threshold
Streptomyces umbrinus	strain=JCM 4521	GCA_014650195.1	67370	67370	type	True	88.0342	1928	2811	95	below_threshold
Streptomyces fructofermentans	strain=JCM 4956	GCA_014651055.1	152141	152141	type	True	86.1478	1694	2811	95	below_threshold
Streptomyces avermitilis	strain=MA-4680	GCA_000009765.2	33903	33903	type	True	84.5529	1561	2811	95	below_threshold
Streptomyces avermitilis	strain=DSM 46492	GCA_001514135.1	33903	33903	type	True	84.4807	1546	2811	95	below_threshold
Streptomyces dengpaensis	strain=XZHG99	GCA_002946835.1	2049881	2049881	type	True	84.4554	1483	2811	95	below_threshold
Streptomyces olivochromogenes	strain=DSM 40451	GCA_001514115.1	1963	1963	type	True	84.4107	1705	2811	95	below_threshold
Streptomyces mirabilis	strain=JCM 4551	GCA_014650275.1	68239	68239	suspected-type	True	84.4071	1677	2811	95	below_threshold
Streptomyces avermitilis	strain=NBRC 14893	GCA_005405965.1	33903	33903	type	True	84.3607	1621	2811	95	below_threshold
Streptomyces albiflavescens	strain=CGMCC 4.7111	GCA_014645835.1	1623582	1623582	type	True	84.3184	1632	2811	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	83.462	1427	2811	95	below_threshold
Streptomyces deccanensis	strain=KCTC 19241	GCA_022385335.1	424188	424188	type	True	83.3461	1594	2811	95	below_threshold
Streptomyces ruber	strain=JCM 3131	GCA_014648075.1	83378	83378	type	True	83.2947	1430	2811	95	below_threshold
Streptomyces prunicolor	strain=NBRC 13075	GCA_000367365.1	67348	67348	type	True	83.2322	1605	2811	95	below_threshold
Streptomyces caniscabiei	strain=NE06-02D	GCA_014930365.1	2746961	2746961	type	True	83.2018	1606	2811	95	below_threshold
Streptomyces glomeratus	strain=DSM 41457	GCA_021462825.1	284452	284452	type	True	82.9985	1300	2811	95	below_threshold
Streptomyces alboniger	strain=NRRL B-1832	GCA_001418385.1	132473	132473	type	True	82.6836	1173	2811	95	below_threshold
Streptomyces alboniger	strain=ATCC 12461	GCA_008704395.1	132473	132473	type	True	82.6786	1310	2811	95	below_threshold
Streptomyces durmitorensis	strain=MS405	GCA_023498005.1	319947	319947	type	True	82.4304	1495	2811	95	below_threshold
Streptomyces boluensis	strain=YC537	GCA_009908195.1	1775135	1775135	type	True	82.1376	1133	2811	95	below_threshold
Streptomyces chilikensis	strain=RC 1830	GCA_001642695.2	1194079	1194079	type	True	81.2057	1105	2811	95	below_threshold
Streptomyces cavourensis	strain=DSM 41795	GCA_006788935.1	67258	67258	type	True	81.002	1224	2811	95	below_threshold
Streptomyces cavourensis	strain=JCM 4298	GCA_014649215.1	67258	67258	type	True	80.9851	1202	2811	95	below_threshold
Streptomyces zagrosensis	strain=CECT 8305	GCA_014203645.1	1042984	1042984	type	True	79.3398	917	2811	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:57,737] [INFO] DFAST Taxonomy check result was written to GCF_001418335.1_ASM141833v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:57,737] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:57,738] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:57,738] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0bd3e15-2da7-47d3-bf87-2adb3dcb1a67/dqc_reference/checkm_data
[2024-01-24 10:58:57,739] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:57,824] [INFO] Task started: CheckM
[2024-01-24 10:58:57,824] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001418335.1_ASM141833v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001418335.1_ASM141833v1_genomic.fna/checkm_input GCF_001418335.1_ASM141833v1_genomic.fna/checkm_result
[2024-01-24 11:00:17,350] [INFO] Task succeeded: CheckM
[2024-01-24 11:00:17,351] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 3.12%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 11:00:17,384] [INFO] ===== Completeness check finished =====
[2024-01-24 11:00:17,384] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:00:17,385] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001418335.1_ASM141833v1_genomic.fna/markers.fasta)
[2024-01-24 11:00:17,385] [INFO] Task started: Blastn
[2024-01-24 11:00:17,385] [INFO] Running command: blastn -query GCF_001418335.1_ASM141833v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge0bd3e15-2da7-47d3-bf87-2adb3dcb1a67/dqc_reference/reference_markers_gtdb.fasta -out GCF_001418335.1_ASM141833v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:00:19,334] [INFO] Task succeeded: Blastn
[2024-01-24 11:00:19,338] [INFO] Selected 11 target genomes.
[2024-01-24 11:00:19,339] [INFO] Target genome list was writen to GCF_001418335.1_ASM141833v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:00:19,366] [INFO] Task started: fastANI
[2024-01-24 11:00:19,366] [INFO] Running command: fastANI --query /var/lib/cwl/stge49b80e9-a571-4be8-8116-061f0a0358f8/GCF_001418335.1_ASM141833v1_genomic.fna.gz --refList GCF_001418335.1_ASM141833v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001418335.1_ASM141833v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:00:46,536] [INFO] Task succeeded: fastANI
[2024-01-24 11:00:46,551] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:00:46,551] [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_001418335.1	s__Streptomyces aurantiacus	100.0	2783	2811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.25	99.25	0.97	0.97	2	conclusive
GCF_014650955.1	s__Streptomyces tauricus	90.237	1956	2811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018070025.1	s__Streptomyces sp018070025	89.8223	2077	2811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003024195.1	s__Streptomyces dioscori	89.7524	2063	2811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019090165.1	s__Streptomyces sp019090165	89.399	1819	2811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016598615.1	s__Streptomyces sp016598615	88.1556	1925	2811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007050945.1	s__Streptomyces sp007050945	88.1534	1923	2811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008905045.1	s__Streptomyces albicerus	87.7154	1843	2811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651055.1	s__Streptomyces fructofermentans	86.1565	1693	2811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011045015.1	s__Streptomyces scabichelini	85.4465	1643	2811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331005.1	s__Streptomyces turgidiscabies	83.2216	1484	2811	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.81	99.67	0.92	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:00:46,553] [INFO] GTDB search result was written to GCF_001418335.1_ASM141833v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:00:46,553] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:00:46,557] [INFO] DFAST_QC result json was written to GCF_001418335.1_ASM141833v1_genomic.fna/dqc_result.json
[2024-01-24 11:00:46,557] [INFO] DFAST_QC completed!
[2024-01-24 11:00:46,557] [INFO] Total running time: 0h3m8s