[2024-01-24 11:58:53,705] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:53,708] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:53,708] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ec3c8d4-e9fb-423b-9d7b-6fb65dd2f997/dqc_reference
[2024-01-24 11:58:54,890] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:54,891] [INFO] Task started: Prodigal
[2024-01-24 11:58:54,891] [INFO] Running command: gunzip -c /var/lib/cwl/stg14cb10a1-6144-4956-a1cc-9e30bf80d088/GCF_013870525.1_ASM1387052v1_genomic.fna.gz | prodigal -d GCF_013870525.1_ASM1387052v1_genomic.fna/cds.fna -a GCF_013870525.1_ASM1387052v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:21,718] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:21,718] [INFO] Task started: HMMsearch
[2024-01-24 11:59:21,718] [INFO] Running command: hmmsearch --tblout GCF_013870525.1_ASM1387052v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ec3c8d4-e9fb-423b-9d7b-6fb65dd2f997/dqc_reference/reference_markers.hmm GCF_013870525.1_ASM1387052v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:22,211] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:22,212] [INFO] Found 6/6 markers.
[2024-01-24 11:59:22,279] [INFO] Query marker FASTA was written to GCF_013870525.1_ASM1387052v1_genomic.fna/markers.fasta
[2024-01-24 11:59:22,279] [INFO] Task started: Blastn
[2024-01-24 11:59:22,279] [INFO] Running command: blastn -query GCF_013870525.1_ASM1387052v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ec3c8d4-e9fb-423b-9d7b-6fb65dd2f997/dqc_reference/reference_markers.fasta -out GCF_013870525.1_ASM1387052v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:23,561] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:23,565] [INFO] Selected 20 target genomes.
[2024-01-24 11:59:23,566] [INFO] Target genome list was writen to GCF_013870525.1_ASM1387052v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:23,596] [INFO] Task started: fastANI
[2024-01-24 11:59:23,596] [INFO] Running command: fastANI --query /var/lib/cwl/stg14cb10a1-6144-4956-a1cc-9e30bf80d088/GCF_013870525.1_ASM1387052v1_genomic.fna.gz --refList GCF_013870525.1_ASM1387052v1_genomic.fna/target_genomes.txt --output GCF_013870525.1_ASM1387052v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:00:07,483] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:07,484] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ec3c8d4-e9fb-423b-9d7b-6fb65dd2f997/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:00:07,484] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ec3c8d4-e9fb-423b-9d7b-6fb65dd2f997/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:00:07,500] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:00:07,501] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:00:07,501] [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
Amycolatopsis pittospori	strain=PIP199	GCA_013870525.1	2749434	2749434	type	True	100.0	2705	2716	95	conclusive
Amycolatopsis umgeniensis	strain=DSM 45272	GCA_014205155.1	336628	336628	type	True	90.1737	2237	2716	95	below_threshold
Amycolatopsis orientalis	strain=KCTC 9412	GCA_000478275.1	31958	31958	type	True	89.9942	2215	2716	95	below_threshold
Amycolatopsis azurea	strain=DSM 43854	GCA_000340415.1	36819	36819	type	True	89.9412	2181	2716	95	below_threshold
Amycolatopsis azurea	strain=DSM 43854	GCA_001995215.1	36819	36819	type	True	89.9143	2227	2716	95	below_threshold
Amycolatopsis alba	strain=DSM 44262	GCA_000384215.1	76020	76020	type	True	89.7759	2223	2716	95	below_threshold
Amycolatopsis alba	strain=DSM 44262	GCA_002234385.1	76020	76020	type	True	89.6877	2077	2716	95	below_threshold
Amycolatopsis thailandensis	strain=JCM 16380	GCA_002234405.1	589330	589330	type	True	89.6136	2082	2716	95	below_threshold
Amycolatopsis regifaucium	strain=GY080	GCA_001613935.1	546365	546365	type	True	89.6029	2053	2716	95	below_threshold
Amycolatopsis japonica	strain=MG417-CF17	GCA_000732925.1	208439	208439	type	True	89.4786	2200	2716	95	below_threshold
Amycolatopsis roodepoortensis	strain=DSM 46661	GCA_014873915.1	700274	700274	type	True	89.472	2149	2716	95	below_threshold
Amycolatopsis keratiniphila subsp. nogabecina	strain=FH 1893	GCA_001953855.1	208442	129921	type	True	89.3983	2159	2716	95	below_threshold
Amycolatopsis lurida	strain=DSM 43134	GCA_900105055.1	31959	31959	type	True	89.3267	2155	2716	95	below_threshold
Amycolatopsis keratiniphila subsp. keratiniphila	strain=DSM 44409	GCA_001620365.2	227715	129921	type	True	89.3264	2179	2716	95	below_threshold
Amycolatopsis lurida	strain=NRRL 2430	GCA_000749465.3	31959	31959	type	True	89.3177	2114	2716	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	81.6974	1597	2716	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	79.7967	1033	2716	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	79.0271	956	2716	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	77.9717	781	2716	95	below_threshold
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	77.8282	775	2716	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:00:07,503] [INFO] DFAST Taxonomy check result was written to GCF_013870525.1_ASM1387052v1_genomic.fna/tc_result.tsv
[2024-01-24 12:00:07,504] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:00:07,504] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:00:07,504] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ec3c8d4-e9fb-423b-9d7b-6fb65dd2f997/dqc_reference/checkm_data
[2024-01-24 12:00:07,505] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:00:07,579] [INFO] Task started: CheckM
[2024-01-24 12:00:07,579] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013870525.1_ASM1387052v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013870525.1_ASM1387052v1_genomic.fna/checkm_input GCF_013870525.1_ASM1387052v1_genomic.fna/checkm_result
[2024-01-24 12:01:20,910] [INFO] Task succeeded: CheckM
[2024-01-24 12:01:20,910] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:01:20,930] [INFO] ===== Completeness check finished =====
[2024-01-24 12:01:20,930] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:01:20,930] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013870525.1_ASM1387052v1_genomic.fna/markers.fasta)
[2024-01-24 12:01:20,930] [INFO] Task started: Blastn
[2024-01-24 12:01:20,930] [INFO] Running command: blastn -query GCF_013870525.1_ASM1387052v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4ec3c8d4-e9fb-423b-9d7b-6fb65dd2f997/dqc_reference/reference_markers_gtdb.fasta -out GCF_013870525.1_ASM1387052v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:01:22,744] [INFO] Task succeeded: Blastn
[2024-01-24 12:01:22,748] [INFO] Selected 15 target genomes.
[2024-01-24 12:01:22,748] [INFO] Target genome list was writen to GCF_013870525.1_ASM1387052v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:01:22,782] [INFO] Task started: fastANI
[2024-01-24 12:01:22,783] [INFO] Running command: fastANI --query /var/lib/cwl/stg14cb10a1-6144-4956-a1cc-9e30bf80d088/GCF_013870525.1_ASM1387052v1_genomic.fna.gz --refList GCF_013870525.1_ASM1387052v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013870525.1_ASM1387052v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:01:59,978] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:59,990] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:01:59,990] [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_013870525.1	s__Amycolatopsis pittospori	100.0	2705	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002849735.1	s__Amycolatopsis sp002849735	90.2601	2275	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014205155.1	s__Amycolatopsis umgeniensis	90.1538	2240	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000478275.1	s__Amycolatopsis orientalis	90.0023	2214	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	96.64	96.64	0.89	0.89	2	-
GCF_001995215.1	s__Amycolatopsis azurea	89.9301	2225	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	100.00	100.00	0.99	0.99	2	-
GCF_014654365.1	s__Amycolatopsis oliviviridis	89.8888	2253	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003947415.1	s__Amycolatopsis sp003947415	89.804	2165	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	96.38	96.38	0.89	0.88	3	-
GCF_000384215.1	s__Amycolatopsis alba	89.7905	2221	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000342005.1	s__Amycolatopsis decaplanina	89.7516	2096	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613935.1	s__Amycolatopsis regifaucium	89.6163	2051	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.99	99.99	0.99	0.99	3	-
GCF_002234405.1	s__Amycolatopsis thailandensis	89.5711	2089	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873915.1	s__Amycolatopsis roodepoortensis	89.4735	2148	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	96.45	96.45	0.88	0.88	2	-
GCF_000732925.1	s__Amycolatopsis japonica	89.4686	2203	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	97.30	96.67	0.90	0.88	4	-
GCF_900105055.1	s__Amycolatopsis lurida	89.3414	2153	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	97.56	95.13	0.93	0.86	3	-
GCF_001620365.2	s__Amycolatopsis keratiniphila	89.3239	2180	2716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	97.78	96.67	0.89	0.86	5	-
--------------------------------------------------------------------------------
[2024-01-24 12:01:59,991] [INFO] GTDB search result was written to GCF_013870525.1_ASM1387052v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:01:59,992] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:01:59,996] [INFO] DFAST_QC result json was written to GCF_013870525.1_ASM1387052v1_genomic.fna/dqc_result.json
[2024-01-24 12:01:59,996] [INFO] DFAST_QC completed!
[2024-01-24 12:01:59,996] [INFO] Total running time: 0h3m6s