[2024-01-24 12:25:20,251] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:25:20,253] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:25:20,253] [INFO] DQC Reference Directory: /var/lib/cwl/stg76f5c55e-a189-49aa-8d63-40c85122bdd6/dqc_reference
[2024-01-24 12:25:21,503] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:25:21,504] [INFO] Task started: Prodigal
[2024-01-24 12:25:21,504] [INFO] Running command: gunzip -c /var/lib/cwl/stgbfefbed7-06b8-4d4b-a766-59a347c19622/GCF_006715045.1_ASM671504v1_genomic.fna.gz | prodigal -d GCF_006715045.1_ASM671504v1_genomic.fna/cds.fna -a GCF_006715045.1_ASM671504v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:25:49,430] [INFO] Task succeeded: Prodigal
[2024-01-24 12:25:49,430] [INFO] Task started: HMMsearch
[2024-01-24 12:25:49,430] [INFO] Running command: hmmsearch --tblout GCF_006715045.1_ASM671504v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg76f5c55e-a189-49aa-8d63-40c85122bdd6/dqc_reference/reference_markers.hmm GCF_006715045.1_ASM671504v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:25:49,805] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:25:49,807] [INFO] Found 6/6 markers.
[2024-01-24 12:25:49,872] [INFO] Query marker FASTA was written to GCF_006715045.1_ASM671504v1_genomic.fna/markers.fasta
[2024-01-24 12:25:49,872] [INFO] Task started: Blastn
[2024-01-24 12:25:49,872] [INFO] Running command: blastn -query GCF_006715045.1_ASM671504v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76f5c55e-a189-49aa-8d63-40c85122bdd6/dqc_reference/reference_markers.fasta -out GCF_006715045.1_ASM671504v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:25:51,109] [INFO] Task succeeded: Blastn
[2024-01-24 12:25:51,114] [INFO] Selected 17 target genomes.
[2024-01-24 12:25:51,115] [INFO] Target genome list was writen to GCF_006715045.1_ASM671504v1_genomic.fna/target_genomes.txt
[2024-01-24 12:25:51,123] [INFO] Task started: fastANI
[2024-01-24 12:25:51,123] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfefbed7-06b8-4d4b-a766-59a347c19622/GCF_006715045.1_ASM671504v1_genomic.fna.gz --refList GCF_006715045.1_ASM671504v1_genomic.fna/target_genomes.txt --output GCF_006715045.1_ASM671504v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:26:19,569] [INFO] Task succeeded: fastANI
[2024-01-24 12:26:19,570] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg76f5c55e-a189-49aa-8d63-40c85122bdd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:26:19,571] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg76f5c55e-a189-49aa-8d63-40c85122bdd6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:26:19,588] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:26:19,588] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:26:19,588] [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 cihanbeyliensis	strain=DSM 45679	GCA_006715045.1	1128664	1128664	type	True	100.0	2477	2477	95	conclusive
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	89.7902	1968	2477	95	below_threshold
Amycolatopsis arida	strain=CGMCC 4.5579	GCA_900115565.1	587909	587909	type	True	81.1266	1175	2477	95	below_threshold
Amycolatopsis arida	strain=DSM 45648	GCA_004365925.1	587909	587909	type	True	81.0909	1181	2477	95	below_threshold
Amycolatopsis nigrescens	strain=CSC17Ta-90	GCA_000384315.1	381445	381445	type	True	80.6313	1294	2477	95	below_threshold
Amycolatopsis anabasis	strain=EGI 650086	GCA_009765355.1	1840409	1840409	type	True	80.1878	1279	2477	95	below_threshold
Amycolatopsis palatopharyngis	strain=DSM 44832	GCA_003385185.1	187982	187982	type	True	80.0899	994	2477	95	below_threshold
Amycolatopsis albispora	strain=WP1	GCA_003312875.1	1804986	1804986	type	True	80.0516	1241	2477	95	below_threshold
Prauserella muralis	strain=DSM 45305	GCA_007993965.1	588067	588067	type	True	79.9505	1084	2477	95	below_threshold
Amycolatopsis magusensis	strain=DSM 45510	GCA_017875555.1	882444	882444	type	True	79.9484	1186	2477	95	below_threshold
Prauserella muralis	strain=DSM 45305	GCA_003202285.1	588067	588067	type	True	79.9181	1090	2477	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	79.5789	974	2477	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	79.494	991	2477	95	below_threshold
Saccharomonospora marina	strain=XMU15	GCA_000244955.1	632569	632569	type	True	79.437	815	2477	95	below_threshold
Amycolatopsis sacchari	strain=DSM 44468	GCA_900114035.1	115433	115433	type	True	79.0919	925	2477	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	78.6023	1079	2477	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	78.0004	751	2477	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:26:19,590] [INFO] DFAST Taxonomy check result was written to GCF_006715045.1_ASM671504v1_genomic.fna/tc_result.tsv
[2024-01-24 12:26:19,590] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:26:19,590] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:26:19,591] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg76f5c55e-a189-49aa-8d63-40c85122bdd6/dqc_reference/checkm_data
[2024-01-24 12:26:19,592] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:26:19,661] [INFO] Task started: CheckM
[2024-01-24 12:26:19,661] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006715045.1_ASM671504v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006715045.1_ASM671504v1_genomic.fna/checkm_input GCF_006715045.1_ASM671504v1_genomic.fna/checkm_result
[2024-01-24 12:27:50,487] [INFO] Task succeeded: CheckM
[2024-01-24 12:27:50,489] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:27:50,517] [INFO] ===== Completeness check finished =====
[2024-01-24 12:27:50,518] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:27:50,518] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006715045.1_ASM671504v1_genomic.fna/markers.fasta)
[2024-01-24 12:27:50,519] [INFO] Task started: Blastn
[2024-01-24 12:27:50,519] [INFO] Running command: blastn -query GCF_006715045.1_ASM671504v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76f5c55e-a189-49aa-8d63-40c85122bdd6/dqc_reference/reference_markers_gtdb.fasta -out GCF_006715045.1_ASM671504v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:27:52,358] [INFO] Task succeeded: Blastn
[2024-01-24 12:27:52,363] [INFO] Selected 16 target genomes.
[2024-01-24 12:27:52,363] [INFO] Target genome list was writen to GCF_006715045.1_ASM671504v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:27:52,429] [INFO] Task started: fastANI
[2024-01-24 12:27:52,429] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfefbed7-06b8-4d4b-a766-59a347c19622/GCF_006715045.1_ASM671504v1_genomic.fna.gz --refList GCF_006715045.1_ASM671504v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006715045.1_ASM671504v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:28:19,956] [INFO] Task succeeded: fastANI
[2024-01-24 12:28:19,976] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:28:19,976] [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_006715045.1	s__Amycolatopsis_D cihanbeyliensis	100.0	2477	2477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis_D	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018885265.1	s__Amycolatopsis_D sp018885265	89.7758	1970	2477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115565.1	s__Yuhushiella arida	81.1573	1168	2477	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	80.6192	1295	2477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016464705.1	s__Saccharomonospora sp016464705	80.3294	1047	2477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765355.1	s__Amycolatopsis anabasis	80.1875	1279	2477	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	80.1727	1060	2477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003312875.1	s__Amycolatopsis albispora	80.0765	1239	2477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385185.1	s__Amycolatopsis_D palatopharyngis	80.0584	998	2477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009429145.1	s__Amycolatopsis sp009429145	80.0197	1227	2477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017309385.1	s__Amycolatopsis sp017309385	79.9524	1247	2477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202285.1	s__Saccharomonospora muralis	79.9084	1096	2477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004214935.1	s__Amycolatopsis suaedae	79.8716	1146	2477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005146945.1	s__Saccharomonospora endophytica	79.6534	1030	2477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	99.14	99.02	0.90	0.90	3	-
GCF_000244955.1	s__Saccharomonospora marina	79.382	816	2477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114035.1	s__Amycolatopsis sacchari	79.0735	930	2477	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:28:19,978] [INFO] GTDB search result was written to GCF_006715045.1_ASM671504v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:28:19,979] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:28:19,983] [INFO] DFAST_QC result json was written to GCF_006715045.1_ASM671504v1_genomic.fna/dqc_result.json
[2024-01-24 12:28:19,983] [INFO] DFAST_QC completed!
[2024-01-24 12:28:19,983] [INFO] Total running time: 0h2m60s