[2024-01-25 19:03:05,493] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:03:05,495] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:03:05,495] [INFO] DQC Reference Directory: /var/lib/cwl/stg4672c3a6-dcb0-426b-9b54-3987e3179f82/dqc_reference
[2024-01-25 19:03:06,615] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:03:06,616] [INFO] Task started: Prodigal
[2024-01-25 19:03:06,616] [INFO] Running command: gunzip -c /var/lib/cwl/stg6fc1f2dd-3316-45cb-80c6-7380e810a431/GCF_030803725.1_ASM3080372v1_genomic.fna.gz | prodigal -d GCF_030803725.1_ASM3080372v1_genomic.fna/cds.fna -a GCF_030803725.1_ASM3080372v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:03:29,344] [INFO] Task succeeded: Prodigal
[2024-01-25 19:03:29,344] [INFO] Task started: HMMsearch
[2024-01-25 19:03:29,344] [INFO] Running command: hmmsearch --tblout GCF_030803725.1_ASM3080372v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4672c3a6-dcb0-426b-9b54-3987e3179f82/dqc_reference/reference_markers.hmm GCF_030803725.1_ASM3080372v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:03:29,632] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:03:29,633] [INFO] Found 6/6 markers.
[2024-01-25 19:03:29,689] [INFO] Query marker FASTA was written to GCF_030803725.1_ASM3080372v1_genomic.fna/markers.fasta
[2024-01-25 19:03:29,689] [INFO] Task started: Blastn
[2024-01-25 19:03:29,689] [INFO] Running command: blastn -query GCF_030803725.1_ASM3080372v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4672c3a6-dcb0-426b-9b54-3987e3179f82/dqc_reference/reference_markers.fasta -out GCF_030803725.1_ASM3080372v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:03:30,920] [INFO] Task succeeded: Blastn
[2024-01-25 19:03:30,923] [INFO] Selected 18 target genomes.
[2024-01-25 19:03:30,923] [INFO] Target genome list was writen to GCF_030803725.1_ASM3080372v1_genomic.fna/target_genomes.txt
[2024-01-25 19:03:30,936] [INFO] Task started: fastANI
[2024-01-25 19:03:30,936] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fc1f2dd-3316-45cb-80c6-7380e810a431/GCF_030803725.1_ASM3080372v1_genomic.fna.gz --refList GCF_030803725.1_ASM3080372v1_genomic.fna/target_genomes.txt --output GCF_030803725.1_ASM3080372v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:04:10,184] [INFO] Task succeeded: fastANI
[2024-01-25 19:04:10,184] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4672c3a6-dcb0-426b-9b54-3987e3179f82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:04:10,185] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4672c3a6-dcb0-426b-9b54-3987e3179f82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:04:10,197] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:04:10,197] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:04:10,198] [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 daghestanicus	strain=NBRC 12762	GCA_020521275.1	66885	66885	suspected-type	True	99.5856	2531	2624	95	conclusive
Streptomyces daghestanicus	strain=JCM 4365	GCA_014649475.1	66885	66885	suspected-type	True	99.5716	2459	2624	95	conclusive
Streptomyces fumanus	strain=JCM 4477	GCA_014655295.1	67302	67302	type	True	87.9738	1825	2624	95	below_threshold
Streptomyces flaveolus	strain=JCM 4032	GCA_014648815.1	67297	67297	type	True	86.7124	1721	2624	95	below_threshold
Streptomyces solaniscabiei	strain=FS70	GCA_020312315.1	2683255	2683255	type	True	86.6618	1699	2624	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	86.5016	1734	2624	95	below_threshold
Streptomyces rubrogriseus	strain=NBRC 15455	GCA_003112595.1	194673	194673	type	True	86.312	1750	2624	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	86.1264	1493	2624	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	85.6136	1672	2624	95	below_threshold
Streptomyces calvus	strain=JCM 4326	GCA_014649315.1	67282	67282	type	True	85.5142	1679	2624	95	below_threshold
Streptomyces calvus	strain=CECT 3271	GCA_014138735.1	67282	67282	type	True	85.5038	1697	2624	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	85.3593	1682	2624	95	below_threshold
Streptomyces albaduncus	strain=JCM 4715	GCA_014650615.1	68172	68172	type	True	85.2949	1654	2624	95	below_threshold
Streptomyces albaduncus	strain=CECT 3226	GCA_014203495.1	68172	68172	type	True	85.1858	1697	2624	95	below_threshold
Streptomyces griseosporeus	strain=JCM 4766	GCA_014656055.1	1910	1910	type	True	85.0698	1685	2624	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	85.0659	1498	2624	95	below_threshold
Streptomyces griseoflavus	strain=JCM 4479	GCA_014649995.1	35619	35619	type	True	85.046	1588	2624	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	84.8983	1479	2624	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:04:10,200] [INFO] DFAST Taxonomy check result was written to GCF_030803725.1_ASM3080372v1_genomic.fna/tc_result.tsv
[2024-01-25 19:04:10,200] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:04:10,201] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:04:10,201] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4672c3a6-dcb0-426b-9b54-3987e3179f82/dqc_reference/checkm_data
[2024-01-25 19:04:10,202] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:04:10,273] [INFO] Task started: CheckM
[2024-01-25 19:04:10,273] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030803725.1_ASM3080372v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030803725.1_ASM3080372v1_genomic.fna/checkm_input GCF_030803725.1_ASM3080372v1_genomic.fna/checkm_result
[2024-01-25 19:07:06,421] [INFO] Task succeeded: CheckM
[2024-01-25 19:07:06,423] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:07:06,455] [INFO] ===== Completeness check finished =====
[2024-01-25 19:07:06,455] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:07:06,456] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030803725.1_ASM3080372v1_genomic.fna/markers.fasta)
[2024-01-25 19:07:06,457] [INFO] Task started: Blastn
[2024-01-25 19:07:06,457] [INFO] Running command: blastn -query GCF_030803725.1_ASM3080372v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4672c3a6-dcb0-426b-9b54-3987e3179f82/dqc_reference/reference_markers_gtdb.fasta -out GCF_030803725.1_ASM3080372v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:07:08,508] [INFO] Task succeeded: Blastn
[2024-01-25 19:07:08,511] [INFO] Selected 18 target genomes.
[2024-01-25 19:07:08,511] [INFO] Target genome list was writen to GCF_030803725.1_ASM3080372v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:07:08,533] [INFO] Task started: fastANI
[2024-01-25 19:07:08,533] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fc1f2dd-3316-45cb-80c6-7380e810a431/GCF_030803725.1_ASM3080372v1_genomic.fna.gz --refList GCF_030803725.1_ASM3080372v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030803725.1_ASM3080372v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:07:47,394] [INFO] Task succeeded: fastANI
[2024-01-25 19:07:47,406] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:07:47,406] [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_014649155.1	s__Streptomyces griseoviridis	99.9782	2558	2624	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.52	99.48	0.96	0.96	3	conclusive
GCF_018614415.1	s__Streptomyces sp018614415	90.126	1858	2624	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014655295.1	s__Streptomyces fumanus	87.9142	1833	2624	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005565.1	s__Streptomyces sp002005565	86.7718	1614	2624	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648815.1	s__Streptomyces flaveolus	86.7338	1718	2624	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002155895.1	s__Streptomyces rochei	86.6168	1511	2624	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.80	98.25	0.91	0.79	28	-
GCA_003248315.1	s__Streptomyces sp003248315	86.5751	1683	2624	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905385.1	s__Streptomyces sp001905385	86.5536	1716	2624	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.01	96.01	0.83	0.83	2	-
GCA_000720845.1	s__Streptomyces sp000720845	86.462	1745	2624	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000717995.1	s__Streptomyces violaceorubidus	86.3309	1696	2624	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	86.1465	1742	2624	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.84	97.03	0.90	0.86	6	-
GCF_000721235.1	s__Streptomyces olivaceus	85.9791	1715	2624	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.53	98.10	0.91	0.89	6	-
GCF_000721605.1	s__Streptomyces sp000721605	85.5559	1673	2624	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905725.1	s__Streptomyces sp001905725	85.5076	1722	2624	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009852415.1	s__Streptomyces sp009852415	85.5026	1755	2624	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069565.1	s__Streptomyces sp018069565	85.4025	1569	2624	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014650015.1	s__Streptomyces griseoloalbus	85.2384	1671	2624	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.17	99.17	0.94	0.94	3	-
GCF_014656055.1	s__Streptomyces griseosporeus	85.1651	1668	2624	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.70	98.69	0.95	0.95	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:07:47,408] [INFO] GTDB search result was written to GCF_030803725.1_ASM3080372v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:07:47,408] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:07:47,412] [INFO] DFAST_QC result json was written to GCF_030803725.1_ASM3080372v1_genomic.fna/dqc_result.json
[2024-01-25 19:07:47,412] [INFO] DFAST_QC completed!
[2024-01-25 19:07:47,412] [INFO] Total running time: 0h4m42s