[2024-01-24 12:06:34,709] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:34,711] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:34,711] [INFO] DQC Reference Directory: /var/lib/cwl/stga338428f-c637-4a11-ac4e-c3687ec5f472/dqc_reference
[2024-01-24 12:06:35,947] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:35,948] [INFO] Task started: Prodigal
[2024-01-24 12:06:35,948] [INFO] Running command: gunzip -c /var/lib/cwl/stg593bc829-9e6e-45e5-b710-69c4a2c88f13/GCF_002240355.1_ASM224035v1_genomic.fna.gz | prodigal -d GCF_002240355.1_ASM224035v1_genomic.fna/cds.fna -a GCF_002240355.1_ASM224035v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:07:15,365] [INFO] Task succeeded: Prodigal
[2024-01-24 12:07:15,365] [INFO] Task started: HMMsearch
[2024-01-24 12:07:15,365] [INFO] Running command: hmmsearch --tblout GCF_002240355.1_ASM224035v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga338428f-c637-4a11-ac4e-c3687ec5f472/dqc_reference/reference_markers.hmm GCF_002240355.1_ASM224035v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:07:15,713] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:07:15,715] [INFO] Found 6/6 markers.
[2024-01-24 12:07:15,779] [INFO] Query marker FASTA was written to GCF_002240355.1_ASM224035v1_genomic.fna/markers.fasta
[2024-01-24 12:07:15,780] [INFO] Task started: Blastn
[2024-01-24 12:07:15,780] [INFO] Running command: blastn -query GCF_002240355.1_ASM224035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga338428f-c637-4a11-ac4e-c3687ec5f472/dqc_reference/reference_markers.fasta -out GCF_002240355.1_ASM224035v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:16,942] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:16,947] [INFO] Selected 13 target genomes.
[2024-01-24 12:07:16,947] [INFO] Target genome list was writen to GCF_002240355.1_ASM224035v1_genomic.fna/target_genomes.txt
[2024-01-24 12:07:16,954] [INFO] Task started: fastANI
[2024-01-24 12:07:16,954] [INFO] Running command: fastANI --query /var/lib/cwl/stg593bc829-9e6e-45e5-b710-69c4a2c88f13/GCF_002240355.1_ASM224035v1_genomic.fna.gz --refList GCF_002240355.1_ASM224035v1_genomic.fna/target_genomes.txt --output GCF_002240355.1_ASM224035v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:36,004] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:36,005] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga338428f-c637-4a11-ac4e-c3687ec5f472/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:36,005] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga338428f-c637-4a11-ac4e-c3687ec5f472/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:36,019] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:07:36,019] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:36,019] [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
Prauserella marina	strain=DSM 45268	GCA_002240355.1	530584	530584	type	True	100.0	2326	2327	95	conclusive
Prauserella marina	strain=DSM 45268	GCA_003182115.1	530584	530584	type	True	99.9901	2311	2327	95	conclusive
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	80.8213	1171	2327	95	below_threshold
Prauserella muralis	strain=DSM 45305	GCA_003202285.1	588067	588067	type	True	80.6665	1117	2327	95	below_threshold
Prauserella muralis	strain=DSM 45305	GCA_007993965.1	588067	588067	type	True	80.6467	1116	2327	95	below_threshold
Saccharomonospora marina	strain=XMU15	GCA_000244955.1	632569	632569	type	True	79.5224	835	2327	95	below_threshold
Saccharomonospora cyanea	strain=NA-134	GCA_000244975.1	40989	40989	type	True	79.1659	722	2327	95	below_threshold
Saccharomonospora glauca	strain=K62	GCA_000243395.3	40990	40990	type	True	78.9819	664	2327	95	below_threshold
Amycolatopsis arida	strain=DSM 45648	GCA_004365925.1	587909	587909	type	True	78.7924	831	2327	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	78.6049	793	2327	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	78.5765	818	2327	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	77.9779	824	2327	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	77.5794	552	2327	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:36,021] [INFO] DFAST Taxonomy check result was written to GCF_002240355.1_ASM224035v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:36,021] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:36,021] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:36,021] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga338428f-c637-4a11-ac4e-c3687ec5f472/dqc_reference/checkm_data
[2024-01-24 12:07:36,022] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:36,091] [INFO] Task started: CheckM
[2024-01-24 12:07:36,092] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002240355.1_ASM224035v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002240355.1_ASM224035v1_genomic.fna/checkm_input GCF_002240355.1_ASM224035v1_genomic.fna/checkm_result
[2024-01-24 12:09:32,420] [INFO] Task succeeded: CheckM
[2024-01-24 12:09:32,422] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:09:32,448] [INFO] ===== Completeness check finished =====
[2024-01-24 12:09:32,449] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:09:32,449] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002240355.1_ASM224035v1_genomic.fna/markers.fasta)
[2024-01-24 12:09:32,449] [INFO] Task started: Blastn
[2024-01-24 12:09:32,450] [INFO] Running command: blastn -query GCF_002240355.1_ASM224035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga338428f-c637-4a11-ac4e-c3687ec5f472/dqc_reference/reference_markers_gtdb.fasta -out GCF_002240355.1_ASM224035v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:09:34,072] [INFO] Task succeeded: Blastn
[2024-01-24 12:09:34,076] [INFO] Selected 10 target genomes.
[2024-01-24 12:09:34,076] [INFO] Target genome list was writen to GCF_002240355.1_ASM224035v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:09:34,084] [INFO] Task started: fastANI
[2024-01-24 12:09:34,084] [INFO] Running command: fastANI --query /var/lib/cwl/stg593bc829-9e6e-45e5-b710-69c4a2c88f13/GCF_002240355.1_ASM224035v1_genomic.fna.gz --refList GCF_002240355.1_ASM224035v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002240355.1_ASM224035v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:09:48,052] [INFO] Task succeeded: fastANI
[2024-01-24 12:09:48,065] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:09:48,065] [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_002240355.1	s__Saccharomonospora marina_A	100.0	2327	2327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_016595675.1	s__Saccharomonospora sp016595675	80.786	1178	2327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003202235.1	s__Saccharomonospora sp003202235	80.7537	1234	2327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005146945.1	s__Saccharomonospora endophytica	80.731	1184	2327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	99.14	99.02	0.90	0.90	3	-
GCF_003202285.1	s__Saccharomonospora muralis	80.6721	1119	2327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016464705.1	s__Saccharomonospora sp016464705	79.8629	968	2327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000244975.1	s__Saccharomonospora cyanea	79.1465	725	2327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000243395.2	s__Saccharomonospora glauca	78.9747	666	2327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Saccharomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004214935.1	s__Amycolatopsis suaedae	78.7814	840	2327	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	78.7137	840	2327	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Yuhushiella	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:09:48,067] [INFO] GTDB search result was written to GCF_002240355.1_ASM224035v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:09:48,068] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:09:48,071] [INFO] DFAST_QC result json was written to GCF_002240355.1_ASM224035v1_genomic.fna/dqc_result.json
[2024-01-24 12:09:48,071] [INFO] DFAST_QC completed!
[2024-01-24 12:09:48,071] [INFO] Total running time: 0h3m13s