[2024-01-24 13:37:15,353] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:15,357] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:15,357] [INFO] DQC Reference Directory: /var/lib/cwl/stgb8b55c27-77ef-4194-b606-72ddb6f3969d/dqc_reference
[2024-01-24 13:37:18,464] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:18,465] [INFO] Task started: Prodigal
[2024-01-24 13:37:18,466] [INFO] Running command: gunzip -c /var/lib/cwl/stgde688dba-8cec-4107-bc1a-3f27e24ba3a6/GCF_013409505.1_ASM1340950v1_genomic.fna.gz | prodigal -d GCF_013409505.1_ASM1340950v1_genomic.fna/cds.fna -a GCF_013409505.1_ASM1340950v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:34,927] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:34,928] [INFO] Task started: HMMsearch
[2024-01-24 13:37:34,928] [INFO] Running command: hmmsearch --tblout GCF_013409505.1_ASM1340950v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb8b55c27-77ef-4194-b606-72ddb6f3969d/dqc_reference/reference_markers.hmm GCF_013409505.1_ASM1340950v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:35,271] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:35,273] [INFO] Found 6/6 markers.
[2024-01-24 13:37:35,336] [INFO] Query marker FASTA was written to GCF_013409505.1_ASM1340950v1_genomic.fna/markers.fasta
[2024-01-24 13:37:35,337] [INFO] Task started: Blastn
[2024-01-24 13:37:35,337] [INFO] Running command: blastn -query GCF_013409505.1_ASM1340950v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8b55c27-77ef-4194-b606-72ddb6f3969d/dqc_reference/reference_markers.fasta -out GCF_013409505.1_ASM1340950v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:36,706] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:36,709] [INFO] Selected 7 target genomes.
[2024-01-24 13:37:36,710] [INFO] Target genome list was writen to GCF_013409505.1_ASM1340950v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:36,715] [INFO] Task started: fastANI
[2024-01-24 13:37:36,715] [INFO] Running command: fastANI --query /var/lib/cwl/stgde688dba-8cec-4107-bc1a-3f27e24ba3a6/GCF_013409505.1_ASM1340950v1_genomic.fna.gz --refList GCF_013409505.1_ASM1340950v1_genomic.fna/target_genomes.txt --output GCF_013409505.1_ASM1340950v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:50,852] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:50,853] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb8b55c27-77ef-4194-b606-72ddb6f3969d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:50,853] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb8b55c27-77ef-4194-b606-72ddb6f3969d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:50,861] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:50,861] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:50,861] [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
Actinomycetospora corticicola	strain=DSM 45772	GCA_013409505.1	663602	663602	type	True	100.0	2054	2055	95	conclusive
Actinomycetospora chiangmaiensis	strain=DSM 45062	GCA_000379625.1	402650	402650	type	True	88.6626	1600	2055	95	below_threshold
Actinomycetospora soli	strain=SF1	GCA_021026295.1	2893887	2893887	type	True	88.4815	1660	2055	95	below_threshold
Actinomycetospora endophytica	strain=TBRC 5722	GCA_021026375.1	2291215	2291215	type	True	83.091	1410	2055	95	below_threshold
Actinomycetospora succinea	strain=DSM 45775	GCA_004363095.1	663603	663603	type	True	81.1567	1223	2055	95	below_threshold
Actinomycetospora cinnamomea	strain=DSM 45771	GCA_003096675.1	663609	663609	type	True	80.7792	1104	2055	95	below_threshold
Amycolatopsis azurea	strain=DSM 43854	GCA_000340415.1	36819	36819	type	True	76.7207	586	2055	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:50,863] [INFO] DFAST Taxonomy check result was written to GCF_013409505.1_ASM1340950v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:50,863] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:50,863] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:50,863] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb8b55c27-77ef-4194-b606-72ddb6f3969d/dqc_reference/checkm_data
[2024-01-24 13:37:50,864] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:50,926] [INFO] Task started: CheckM
[2024-01-24 13:37:50,926] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013409505.1_ASM1340950v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013409505.1_ASM1340950v1_genomic.fna/checkm_input GCF_013409505.1_ASM1340950v1_genomic.fna/checkm_result
[2024-01-24 13:39:29,294] [INFO] Task succeeded: CheckM
[2024-01-24 13:39:29,296] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:39:29,377] [INFO] ===== Completeness check finished =====
[2024-01-24 13:39:29,378] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:39:29,378] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013409505.1_ASM1340950v1_genomic.fna/markers.fasta)
[2024-01-24 13:39:29,378] [INFO] Task started: Blastn
[2024-01-24 13:39:29,379] [INFO] Running command: blastn -query GCF_013409505.1_ASM1340950v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8b55c27-77ef-4194-b606-72ddb6f3969d/dqc_reference/reference_markers_gtdb.fasta -out GCF_013409505.1_ASM1340950v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:39:31,388] [INFO] Task succeeded: Blastn
[2024-01-24 13:39:31,392] [INFO] Selected 8 target genomes.
[2024-01-24 13:39:31,392] [INFO] Target genome list was writen to GCF_013409505.1_ASM1340950v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:39:31,400] [INFO] Task started: fastANI
[2024-01-24 13:39:31,400] [INFO] Running command: fastANI --query /var/lib/cwl/stgde688dba-8cec-4107-bc1a-3f27e24ba3a6/GCF_013409505.1_ASM1340950v1_genomic.fna.gz --refList GCF_013409505.1_ASM1340950v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013409505.1_ASM1340950v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:39:44,752] [INFO] Task succeeded: fastANI
[2024-01-24 13:39:44,761] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:39:44,762] [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_013409505.1	s__Actinomycetospora corticicola	100.0	2054	2055	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000379625.1	s__Actinomycetospora chiangmaiensis	88.6539	1601	2055	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012933465.1	s__Actinomycetospora sp012933465	83.4779	1394	2055	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805495.1	s__Actinomycetospora sp902805495	81.4321	763	2055	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363095.1	s__Actinomycetospora succinea	81.1913	1218	2055	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096675.1	s__Actinomycetospora cinnamomea	80.7394	1111	2055	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794615.1	s__Pseudonocardia sp016794615	77.5874	539	2055	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014654365.1	s__Amycolatopsis oliviviridis	76.69	585	2055	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 13:39:44,764] [INFO] GTDB search result was written to GCF_013409505.1_ASM1340950v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:39:44,765] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:39:44,770] [INFO] DFAST_QC result json was written to GCF_013409505.1_ASM1340950v1_genomic.fna/dqc_result.json
[2024-01-24 13:39:44,770] [INFO] DFAST_QC completed!
[2024-01-24 13:39:44,771] [INFO] Total running time: 0h2m29s