[2024-01-24 12:45:18,750] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:18,752] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:18,752] [INFO] DQC Reference Directory: /var/lib/cwl/stg98968089-af7b-4760-9a27-1e86850ff67d/dqc_reference
[2024-01-24 12:45:19,902] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:19,903] [INFO] Task started: Prodigal
[2024-01-24 12:45:19,903] [INFO] Running command: gunzip -c /var/lib/cwl/stg0d137939-a128-4ea0-a157-6fe27d85f2da/GCF_004214935.1_ASM421493v1_genomic.fna.gz | prodigal -d GCF_004214935.1_ASM421493v1_genomic.fna/cds.fna -a GCF_004214935.1_ASM421493v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:46,257] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:46,258] [INFO] Task started: HMMsearch
[2024-01-24 12:45:46,258] [INFO] Running command: hmmsearch --tblout GCF_004214935.1_ASM421493v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98968089-af7b-4760-9a27-1e86850ff67d/dqc_reference/reference_markers.hmm GCF_004214935.1_ASM421493v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:46,622] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:46,624] [INFO] Found 6/6 markers.
[2024-01-24 12:45:46,687] [INFO] Query marker FASTA was written to GCF_004214935.1_ASM421493v1_genomic.fna/markers.fasta
[2024-01-24 12:45:46,687] [INFO] Task started: Blastn
[2024-01-24 12:45:46,688] [INFO] Running command: blastn -query GCF_004214935.1_ASM421493v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98968089-af7b-4760-9a27-1e86850ff67d/dqc_reference/reference_markers.fasta -out GCF_004214935.1_ASM421493v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:48,016] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:48,020] [INFO] Selected 21 target genomes.
[2024-01-24 12:45:48,021] [INFO] Target genome list was writen to GCF_004214935.1_ASM421493v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:48,080] [INFO] Task started: fastANI
[2024-01-24 12:45:48,080] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d137939-a128-4ea0-a157-6fe27d85f2da/GCF_004214935.1_ASM421493v1_genomic.fna.gz --refList GCF_004214935.1_ASM421493v1_genomic.fna/target_genomes.txt --output GCF_004214935.1_ASM421493v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:46:31,021] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:31,022] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98968089-af7b-4760-9a27-1e86850ff67d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:46:31,022] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98968089-af7b-4760-9a27-1e86850ff67d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:46:31,041] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:46:31,041] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:46:31,041] [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 suaedae	strain=8-3EHSu	GCA_004214935.1	2510978	2510978	type	True	100.0	2495	2496	95	conclusive
Amycolatopsis albispora	strain=WP1	GCA_003312875.1	1804986	1804986	type	True	81.4005	1503	2496	95	below_threshold
Amycolatopsis magusensis	strain=DSM 45510	GCA_017875555.1	882444	882444	type	True	81.2099	1454	2496	95	below_threshold
Amycolatopsis arida	strain=DSM 45648	GCA_004365925.1	587909	587909	type	True	80.6687	1148	2496	95	below_threshold
Amycolatopsis arida	strain=CGMCC 4.5579	GCA_900115565.1	587909	587909	type	True	80.642	1155	2496	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	80.5693	1139	2496	95	below_threshold
Amycolatopsis nigrescens	strain=CSC17Ta-90	GCA_000384315.1	381445	381445	type	True	80.4374	1364	2496	95	below_threshold
Amycolatopsis anabasis	strain=EGI 650086	GCA_009765355.1	1840409	1840409	type	True	80.3149	1343	2496	95	below_threshold
Amycolatopsis australiensis	strain=DSM 44671	GCA_900119165.1	546364	546364	type	True	80.174	1296	2496	95	below_threshold
Amycolatopsis bartoniae	strain=DSM 45807	GCA_014191255.1	941986	941986	type	True	80.0962	1035	2496	95	below_threshold
Amycolatopsis bartoniae	strain=DSM 45807	GCA_007713755.1	941986	941986	type	True	80.0429	1039	2496	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	79.9448	1179	2496	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	79.9123	1089	2496	95	below_threshold
Amycolatopsis vastitatis	strain=H5	GCA_002234595.1	1905142	1905142	type	True	79.8773	1280	2496	95	below_threshold
Amycolatopsis balhimycina	strain=DSM 44591	GCA_000384295.1	208443	208443	type	True	79.791	1288	2496	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	79.7898	1317	2496	95	below_threshold
Amycolatopsis kentuckyensis	strain=NRRL B-24129	GCA_002155975.1	218823	218823	type	True	79.7768	1231	2496	95	below_threshold
Amycolatopsis acididurans	strain=K13G38	GCA_012328925.1	2724524	2724524	type	True	79.7111	1032	2496	95	below_threshold
Amycolatopsis sulphurea	strain=DSM 46092	GCA_002564045.1	76022	76022	type	True	79.5721	952	2496	95	below_threshold
Saccharomonospora cyanea	strain=NA-134	GCA_000244975.1	40989	40989	type	True	78.8992	774	2496	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	78.4095	870	2496	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:46:31,043] [INFO] DFAST Taxonomy check result was written to GCF_004214935.1_ASM421493v1_genomic.fna/tc_result.tsv
[2024-01-24 12:46:31,043] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:46:31,044] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:46:31,044] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98968089-af7b-4760-9a27-1e86850ff67d/dqc_reference/checkm_data
[2024-01-24 12:46:31,044] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:46:31,116] [INFO] Task started: CheckM
[2024-01-24 12:46:31,116] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004214935.1_ASM421493v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004214935.1_ASM421493v1_genomic.fna/checkm_input GCF_004214935.1_ASM421493v1_genomic.fna/checkm_result
[2024-01-24 12:47:55,641] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:55,642] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:55,666] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:55,666] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:55,666] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004214935.1_ASM421493v1_genomic.fna/markers.fasta)
[2024-01-24 12:47:55,667] [INFO] Task started: Blastn
[2024-01-24 12:47:55,667] [INFO] Running command: blastn -query GCF_004214935.1_ASM421493v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg98968089-af7b-4760-9a27-1e86850ff67d/dqc_reference/reference_markers_gtdb.fasta -out GCF_004214935.1_ASM421493v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:57,796] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:57,800] [INFO] Selected 15 target genomes.
[2024-01-24 12:47:57,800] [INFO] Target genome list was writen to GCF_004214935.1_ASM421493v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:57,812] [INFO] Task started: fastANI
[2024-01-24 12:47:57,813] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d137939-a128-4ea0-a157-6fe27d85f2da/GCF_004214935.1_ASM421493v1_genomic.fna.gz --refList GCF_004214935.1_ASM421493v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004214935.1_ASM421493v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:48:30,522] [INFO] Task succeeded: fastANI
[2024-01-24 12:48:30,537] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:48:30,537] [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_004214935.1	s__Amycolatopsis suaedae	100.0	2495	2496	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_017309385.1	s__Amycolatopsis sp017309385	81.4982	1495	2496	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003312875.1	s__Amycolatopsis albispora	81.3676	1509	2496	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009429145.1	s__Amycolatopsis sp009429145	81.2836	1531	2496	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017875555.1	s__Amycolatopsis magusensis	81.1709	1461	2496	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115565.1	s__Yuhushiella arida	80.657	1152	2496	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Yuhushiella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000384315.1	s__Amycolatopsis nigrescens	80.4216	1368	2496	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765355.1	s__Amycolatopsis anabasis	80.3504	1334	2496	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003001955.1	s__Saccharomonospora shujinwangii	80.3058	1072	2496	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119165.1	s__Amycolatopsis australiensis	80.1773	1291	2496	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002262875.1	s__Amycolatopsis antarctica	80.1191	1020	2496	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014191255.1	s__Amycolatopsis bartoniae	80.0784	1038	2496	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.98	99.98	0.99	0.99	3	-
GCF_018736145.1	s__Amycolatopsis sp018736145	79.8503	1311	2496	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012328925.1	s__Amycolatopsis acididurans	79.6869	1037	2496	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000244975.1	s__Saccharomonospora cyanea	78.8946	775	2496	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:48:30,539] [INFO] GTDB search result was written to GCF_004214935.1_ASM421493v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:48:30,539] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:48:30,543] [INFO] DFAST_QC result json was written to GCF_004214935.1_ASM421493v1_genomic.fna/dqc_result.json
[2024-01-24 12:48:30,543] [INFO] DFAST_QC completed!
[2024-01-24 12:48:30,543] [INFO] Total running time: 0h3m12s