[2024-01-24 12:23:03,261] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:03,262] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:03,262] [INFO] DQC Reference Directory: /var/lib/cwl/stge241ea08-3f6f-49de-b5f6-25c6026138f7/dqc_reference
[2024-01-24 12:23:06,639] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:06,639] [INFO] Task started: Prodigal
[2024-01-24 12:23:06,640] [INFO] Running command: gunzip -c /var/lib/cwl/stg28451e0f-6876-4606-b75f-69a5ee42ccf3/GCF_014655475.1_ASM1465547v1_genomic.fna.gz | prodigal -d GCF_014655475.1_ASM1465547v1_genomic.fna/cds.fna -a GCF_014655475.1_ASM1465547v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:26,627] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:26,627] [INFO] Task started: HMMsearch
[2024-01-24 12:23:26,627] [INFO] Running command: hmmsearch --tblout GCF_014655475.1_ASM1465547v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge241ea08-3f6f-49de-b5f6-25c6026138f7/dqc_reference/reference_markers.hmm GCF_014655475.1_ASM1465547v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:26,918] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:26,919] [INFO] Found 6/6 markers.
[2024-01-24 12:23:26,974] [INFO] Query marker FASTA was written to GCF_014655475.1_ASM1465547v1_genomic.fna/markers.fasta
[2024-01-24 12:23:26,974] [INFO] Task started: Blastn
[2024-01-24 12:23:26,974] [INFO] Running command: blastn -query GCF_014655475.1_ASM1465547v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge241ea08-3f6f-49de-b5f6-25c6026138f7/dqc_reference/reference_markers.fasta -out GCF_014655475.1_ASM1465547v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:28,231] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:28,233] [INFO] Selected 22 target genomes.
[2024-01-24 12:23:28,233] [INFO] Target genome list was writen to GCF_014655475.1_ASM1465547v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:28,239] [INFO] Task started: fastANI
[2024-01-24 12:23:28,239] [INFO] Running command: fastANI --query /var/lib/cwl/stg28451e0f-6876-4606-b75f-69a5ee42ccf3/GCF_014655475.1_ASM1465547v1_genomic.fna.gz --refList GCF_014655475.1_ASM1465547v1_genomic.fna/target_genomes.txt --output GCF_014655475.1_ASM1465547v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:24:10,563] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:10,563] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge241ea08-3f6f-49de-b5f6-25c6026138f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:24:10,564] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge241ea08-3f6f-49de-b5f6-25c6026138f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:24:10,576] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:24:10,576] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:24:10,576] [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 griseoflavus	strain=JCM 4479	GCA_014649995.1	35619	35619	type	True	88.2699	1822	2520	95	below_threshold
Streptomyces malachitofuscus	strain=JCM 4493	GCA_014650055.1	67322	67322	type	True	88.2257	1838	2520	95	below_threshold
Streptomyces pilosus	strain=JCM 4403	GCA_014649835.1	28893	28893	type	True	88.1073	1841	2520	95	below_threshold
Streptomyces capillispiralis	strain=JCM 5075	GCA_014656315.1	68182	68182	type	True	88.0772	1822	2520	95	below_threshold
Streptomyces capillispiralis	strain=DSM 41695	GCA_007829875.1	68182	68182	type	True	88.0603	1858	2520	95	below_threshold
Streptomyces calvus	strain=JCM 4326	GCA_014649315.1	67282	67282	type	True	87.9156	1832	2520	95	below_threshold
Streptomyces calvus	strain=CECT 3271	GCA_014138735.1	67282	67282	type	True	87.8971	1837	2520	95	below_threshold
Streptomyces griseostramineus	strain=JCM 4385	GCA_014649635.1	66898	66898	suspected-type	True	87.8023	1820	2520	95	below_threshold
Streptomyces griseostramineus	strain=CECT 3273	GCA_014203535.1	66898	66898	suspected-type	True	87.7912	1830	2520	95	below_threshold
Streptomyces viridosporus	strain=NRRL 2414	GCA_002078235.1	67581	67581	type	True	87.3537	1493	2520	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	85.7853	1652	2520	95	below_threshold
Streptomyces griseicoloratus	strain=TRM S81-3	GCA_014534645.1	2752516	2752516	type	True	85.7576	1680	2520	95	below_threshold
Streptomyces viridiviolaceus	strain=JCM 4855	GCA_014650995.1	68282	68282	type	True	85.6656	1667	2520	95	below_threshold
Streptomyces flaveolus	strain=JCM 4032	GCA_014648815.1	67297	67297	type	True	85.6242	1670	2520	95	below_threshold
Streptomyces tendae	strain=JCM 4610	GCA_014650435.1	1932	1932	type	True	85.4708	1710	2520	95	below_threshold
Streptomyces indiaensis	strain=DSM 43803	GCA_021474405.1	284033	284033	type	True	85.4378	1528	2520	95	below_threshold
Streptomyces anthocyanicus	strain=JCM 5058	GCA_014651155.1	68174	68174	type	True	85.3104	1733	2520	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	85.2635	1444	2520	95	below_threshold
Streptomyces mutabilis	strain=JCM 4400	GCA_014649815.1	67332	67332	type	True	85.1243	1644	2520	95	below_threshold
Streptomyces nigra	strain=452	GCA_003074055.1	1827580	1827580	type	True	84.9719	1662	2520	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	84.8577	1461	2520	95	below_threshold
Streptomyces blattellae	strain=TRM63209	GCA_009709555.1	2569855	2569855	type	True	84.1384	1492	2520	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:24:10,578] [INFO] DFAST Taxonomy check result was written to GCF_014655475.1_ASM1465547v1_genomic.fna/tc_result.tsv
[2024-01-24 12:24:10,579] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:24:10,579] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:24:10,579] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge241ea08-3f6f-49de-b5f6-25c6026138f7/dqc_reference/checkm_data
[2024-01-24 12:24:10,580] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:24:10,648] [INFO] Task started: CheckM
[2024-01-24 12:24:10,648] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014655475.1_ASM1465547v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014655475.1_ASM1465547v1_genomic.fna/checkm_input GCF_014655475.1_ASM1465547v1_genomic.fna/checkm_result
[2024-01-24 12:26:04,140] [INFO] Task succeeded: CheckM
[2024-01-24 12:26:04,141] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:26:04,159] [INFO] ===== Completeness check finished =====
[2024-01-24 12:26:04,159] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:26:04,160] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014655475.1_ASM1465547v1_genomic.fna/markers.fasta)
[2024-01-24 12:26:04,160] [INFO] Task started: Blastn
[2024-01-24 12:26:04,160] [INFO] Running command: blastn -query GCF_014655475.1_ASM1465547v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge241ea08-3f6f-49de-b5f6-25c6026138f7/dqc_reference/reference_markers_gtdb.fasta -out GCF_014655475.1_ASM1465547v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:26:06,199] [INFO] Task succeeded: Blastn
[2024-01-24 12:26:06,202] [INFO] Selected 7 target genomes.
[2024-01-24 12:26:06,202] [INFO] Target genome list was writen to GCF_014655475.1_ASM1465547v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:26:06,206] [INFO] Task started: fastANI
[2024-01-24 12:26:06,206] [INFO] Running command: fastANI --query /var/lib/cwl/stg28451e0f-6876-4606-b75f-69a5ee42ccf3/GCF_014655475.1_ASM1465547v1_genomic.fna.gz --refList GCF_014655475.1_ASM1465547v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014655475.1_ASM1465547v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:26:21,036] [INFO] Task succeeded: fastANI
[2024-01-24 12:26:21,042] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:26:21,042] [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_014650475.1	s__Streptomyces albogriseolus	98.5718	2311	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.59	97.23	0.93	0.90	7	conclusive
GCA_014656175.1	s__Streptomyces werraensis	94.5895	2042	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014649575.1	s__Streptomyces griseoincarnatus	94.3433	1995	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.374	98.24	97.52	0.91	0.85	21	-
GCA_014649355.1	s__Streptomyces althioticus	94.0719	2020	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.374	98.43	96.72	0.91	0.83	9	-
GCA_014655195.1	s__Streptomyces cellulosae	94.0051	2028	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.05	95.87	0.87	0.85	11	-
GCA_002154585.1	s__Streptomyces pseudogriseolus	93.5699	1622	2520	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.58	96.58	0.90	0.87	9	-
GCF_002899455.1	s__Streptomyces sp002899455	93.1845	1920	2520	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 12:26:21,043] [INFO] GTDB search result was written to GCF_014655475.1_ASM1465547v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:26:21,044] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:26:21,047] [INFO] DFAST_QC result json was written to GCF_014655475.1_ASM1465547v1_genomic.fna/dqc_result.json
[2024-01-24 12:26:21,047] [INFO] DFAST_QC completed!
[2024-01-24 12:26:21,047] [INFO] Total running time: 0h3m18s