[2024-01-25 19:06:50,709] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:06:50,711] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:06:50,711] [INFO] DQC Reference Directory: /var/lib/cwl/stg955f370d-b723-4005-9e43-ea5da74c862d/dqc_reference
[2024-01-25 19:06:51,882] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:06:51,885] [INFO] Task started: Prodigal
[2024-01-25 19:06:51,885] [INFO] Running command: gunzip -c /var/lib/cwl/stg98c3d1c0-2051-4cc7-a9c8-345147fe5c73/GCF_000973705.1_ASM97370v1_genomic.fna.gz | prodigal -d GCF_000973705.1_ASM97370v1_genomic.fna/cds.fna -a GCF_000973705.1_ASM97370v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:06:57,489] [INFO] Task succeeded: Prodigal
[2024-01-25 19:06:57,490] [INFO] Task started: HMMsearch
[2024-01-25 19:06:57,490] [INFO] Running command: hmmsearch --tblout GCF_000973705.1_ASM97370v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg955f370d-b723-4005-9e43-ea5da74c862d/dqc_reference/reference_markers.hmm GCF_000973705.1_ASM97370v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:06:57,770] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:06:57,771] [INFO] Found 6/6 markers.
[2024-01-25 19:06:57,802] [INFO] Query marker FASTA was written to GCF_000973705.1_ASM97370v1_genomic.fna/markers.fasta
[2024-01-25 19:06:57,802] [INFO] Task started: Blastn
[2024-01-25 19:06:57,802] [INFO] Running command: blastn -query GCF_000973705.1_ASM97370v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg955f370d-b723-4005-9e43-ea5da74c862d/dqc_reference/reference_markers.fasta -out GCF_000973705.1_ASM97370v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:06:58,345] [INFO] Task succeeded: Blastn
[2024-01-25 19:06:58,348] [INFO] Selected 10 target genomes.
[2024-01-25 19:06:58,349] [INFO] Target genome list was writen to GCF_000973705.1_ASM97370v1_genomic.fna/target_genomes.txt
[2024-01-25 19:06:58,353] [INFO] Task started: fastANI
[2024-01-25 19:06:58,353] [INFO] Running command: fastANI --query /var/lib/cwl/stg98c3d1c0-2051-4cc7-a9c8-345147fe5c73/GCF_000973705.1_ASM97370v1_genomic.fna.gz --refList GCF_000973705.1_ASM97370v1_genomic.fna/target_genomes.txt --output GCF_000973705.1_ASM97370v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:07:08,951] [INFO] Task succeeded: fastANI
[2024-01-25 19:07:08,952] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg955f370d-b723-4005-9e43-ea5da74c862d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:07:08,952] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg955f370d-b723-4005-9e43-ea5da74c862d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:07:08,960] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-25 19:07:08,960] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:07:08,960] [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
Clostridium sporogenes	strain=NCIMB 10696	GCA_000973705.1	1509	1509	type	True	100.0	1379	1380	95	conclusive
Clostridium sporogenes	strain=DSM 795	GCA_001020205.1	1509	1509	type	True	99.9989	1379	1380	95	conclusive
Clostridium sporogenes	strain=NCTC13020	GCA_900461305.1	1509	1509	type	True	99.9972	1378	1380	95	conclusive
Clostridium sporogenes	strain=DSM 795	GCA_000685115.1	1509	1509	type	True	99.9902	1357	1380	95	conclusive
Clostridium sporogenes	strain=ATCC 3584	GCA_002008145.1	1509	1509	type	True	99.9812	1352	1380	95	conclusive
Clostridium tetanomorphum	strain=DSM 4474	GCA_017873215.1	1553	1553	type	True	77.8707	357	1380	95	below_threshold
Clostridium muellerianum	strain=P21	GCA_012926525.1	2716538	2716538	type	True	77.4126	329	1380	95	below_threshold
Clostridium acetireducens	strain=DSM 10703	GCA_001758365.1	76489	76489	type	True	77.2307	250	1380	95	below_threshold
Clostridium liquoris	strain=DSM 100320	GCA_002995785.1	1289519	1289519	type	True	76.8661	219	1380	95	below_threshold
Oceanirhabdus seepicola	strain=ZWT	GCA_023684385.1	2828781	2828781	type	True	76.1668	145	1380	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:07:08,962] [INFO] DFAST Taxonomy check result was written to GCF_000973705.1_ASM97370v1_genomic.fna/tc_result.tsv
[2024-01-25 19:07:08,963] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:07:08,963] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:07:08,963] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg955f370d-b723-4005-9e43-ea5da74c862d/dqc_reference/checkm_data
[2024-01-25 19:07:08,964] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:07:09,007] [INFO] Task started: CheckM
[2024-01-25 19:07:09,007] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000973705.1_ASM97370v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000973705.1_ASM97370v1_genomic.fna/checkm_input GCF_000973705.1_ASM97370v1_genomic.fna/checkm_result
[2024-01-25 19:07:30,204] [INFO] Task succeeded: CheckM
[2024-01-25 19:07:30,205] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:07:30,220] [INFO] ===== Completeness check finished =====
[2024-01-25 19:07:30,220] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:07:30,221] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000973705.1_ASM97370v1_genomic.fna/markers.fasta)
[2024-01-25 19:07:30,221] [INFO] Task started: Blastn
[2024-01-25 19:07:30,221] [INFO] Running command: blastn -query GCF_000973705.1_ASM97370v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg955f370d-b723-4005-9e43-ea5da74c862d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000973705.1_ASM97370v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:07:30,977] [INFO] Task succeeded: Blastn
[2024-01-25 19:07:30,981] [INFO] Selected 5 target genomes.
[2024-01-25 19:07:30,981] [INFO] Target genome list was writen to GCF_000973705.1_ASM97370v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:07:30,989] [INFO] Task started: fastANI
[2024-01-25 19:07:30,989] [INFO] Running command: fastANI --query /var/lib/cwl/stg98c3d1c0-2051-4cc7-a9c8-345147fe5c73/GCF_000973705.1_ASM97370v1_genomic.fna.gz --refList GCF_000973705.1_ASM97370v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000973705.1_ASM97370v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:07:37,172] [INFO] Task succeeded: fastANI
[2024-01-25 19:07:37,176] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:07:37,176] [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_001020205.1	s__Clostridium_F sporogenes	99.9989	1379	1380	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	99.24	98.80	0.94	0.88	81	conclusive
GCF_001889325.1	s__Clostridium_F botulinum_A	94.3815	1147	1380	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	95.92	95.51	0.89	0.85	52	-
GCF_001276985.1	s__Clostridium_F botulinum	92.0028	1085	1380	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	97.69	95.97	0.92	0.83	213	-
GCF_001276215.1	s__Clostridium_F sp001276215	89.4754	1010	1380	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	97.32	95.44	0.88	0.82	10	-
GCF_002008345.1	s__Clostridium_F tepidum	88.3799	826	1380	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium_F	95.0	99.70	99.54	0.93	0.92	5	-
--------------------------------------------------------------------------------
[2024-01-25 19:07:37,178] [INFO] GTDB search result was written to GCF_000973705.1_ASM97370v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:07:37,178] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:07:37,180] [INFO] DFAST_QC result json was written to GCF_000973705.1_ASM97370v1_genomic.fna/dqc_result.json
[2024-01-25 19:07:37,180] [INFO] DFAST_QC completed!
[2024-01-25 19:07:37,180] [INFO] Total running time: 0h0m46s