[2024-01-24 12:34:20,219] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:34:20,222] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:34:20,222] [INFO] DQC Reference Directory: /var/lib/cwl/stgace41eb0-14f3-4dd8-85f7-e4b21b82f4b8/dqc_reference
[2024-01-24 12:34:21,519] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:34:21,521] [INFO] Task started: Prodigal
[2024-01-24 12:34:21,521] [INFO] Running command: gunzip -c /var/lib/cwl/stgaffc49a4-4454-4700-9024-b3f830382f4b/GCF_003325355.1_ASM332535v1_genomic.fna.gz | prodigal -d GCF_003325355.1_ASM332535v1_genomic.fna/cds.fna -a GCF_003325355.1_ASM332535v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:34:59,878] [INFO] Task succeeded: Prodigal
[2024-01-24 12:34:59,878] [INFO] Task started: HMMsearch
[2024-01-24 12:34:59,878] [INFO] Running command: hmmsearch --tblout GCF_003325355.1_ASM332535v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgace41eb0-14f3-4dd8-85f7-e4b21b82f4b8/dqc_reference/reference_markers.hmm GCF_003325355.1_ASM332535v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:35:00,206] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:35:00,208] [INFO] Found 6/6 markers.
[2024-01-24 12:35:00,263] [INFO] Query marker FASTA was written to GCF_003325355.1_ASM332535v1_genomic.fna/markers.fasta
[2024-01-24 12:35:00,263] [INFO] Task started: Blastn
[2024-01-24 12:35:00,263] [INFO] Running command: blastn -query GCF_003325355.1_ASM332535v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgace41eb0-14f3-4dd8-85f7-e4b21b82f4b8/dqc_reference/reference_markers.fasta -out GCF_003325355.1_ASM332535v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:35:00,832] [INFO] Task succeeded: Blastn
[2024-01-24 12:35:00,836] [INFO] Selected 15 target genomes.
[2024-01-24 12:35:00,837] [INFO] Target genome list was writen to GCF_003325355.1_ASM332535v1_genomic.fna/target_genomes.txt
[2024-01-24 12:35:00,844] [INFO] Task started: fastANI
[2024-01-24 12:35:00,844] [INFO] Running command: fastANI --query /var/lib/cwl/stgaffc49a4-4454-4700-9024-b3f830382f4b/GCF_003325355.1_ASM332535v1_genomic.fna.gz --refList GCF_003325355.1_ASM332535v1_genomic.fna/target_genomes.txt --output GCF_003325355.1_ASM332535v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:35:17,852] [INFO] Task succeeded: fastANI
[2024-01-24 12:35:17,853] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgace41eb0-14f3-4dd8-85f7-e4b21b82f4b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:35:17,854] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgace41eb0-14f3-4dd8-85f7-e4b21b82f4b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:35:17,867] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:35:17,868] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:35:17,868] [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
Runella rosea	strain=HYN0085	GCA_003325355.1	2259595	2259595	type	True	100.0	2379	2384	95	conclusive
Runella aurantiaca	strain=YX9	GCA_003339505.1	2282308	2282308	type	True	92.0316	1976	2384	95	below_threshold
Runella slithyformis	strain=DSM 19594	GCA_000218895.1	106	106	type	True	81.5817	1408	2384	95	below_threshold
Runella limosa	strain=DSM 17973	GCA_000482465.1	370978	370978	type	True	77.5857	598	2384	95	below_threshold
Runella zeae	strain=DSM 19591	GCA_000423565.1	94255	94255	type	True	77.5649	629	2384	95	below_threshold
Runella defluvii	strain=DSM 17976	GCA_014195535.1	370973	370973	type	True	77.5141	617	2384	95	below_threshold
Spirosoma radiotolerans	strain=DG5A	GCA_000974425.1	1379870	1379870	type	True	76.022	71	2384	95	below_threshold
Spirosoma arboris	strain=HMF4905	GCA_009754945.1	2682092	2682092	type	True	75.4945	68	2384	95	below_threshold
Larkinella arboricola	strain=DSM 21851	GCA_003259745.1	643671	643671	type	True	75.4102	76	2384	95	below_threshold
Spirosoma endophyticum	strain=DSM 26130	GCA_900112365.1	662367	662367	type	True	75.3249	68	2384	95	below_threshold
Larkinella humicola	strain=MA1	GCA_008727875.1	2607654	2607654	type	True	75.3238	88	2384	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:35:17,869] [INFO] DFAST Taxonomy check result was written to GCF_003325355.1_ASM332535v1_genomic.fna/tc_result.tsv
[2024-01-24 12:35:17,870] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:35:17,870] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:35:17,870] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgace41eb0-14f3-4dd8-85f7-e4b21b82f4b8/dqc_reference/checkm_data
[2024-01-24 12:35:17,871] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:35:17,941] [INFO] Task started: CheckM
[2024-01-24 12:35:17,941] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003325355.1_ASM332535v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003325355.1_ASM332535v1_genomic.fna/checkm_input GCF_003325355.1_ASM332535v1_genomic.fna/checkm_result
[2024-01-24 12:37:00,441] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:00,443] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:00,467] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:00,467] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:00,468] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003325355.1_ASM332535v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:00,468] [INFO] Task started: Blastn
[2024-01-24 12:37:00,468] [INFO] Running command: blastn -query GCF_003325355.1_ASM332535v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgace41eb0-14f3-4dd8-85f7-e4b21b82f4b8/dqc_reference/reference_markers_gtdb.fasta -out GCF_003325355.1_ASM332535v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:01,180] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:01,183] [INFO] Selected 8 target genomes.
[2024-01-24 12:37:01,184] [INFO] Target genome list was writen to GCF_003325355.1_ASM332535v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:01,189] [INFO] Task started: fastANI
[2024-01-24 12:37:01,189] [INFO] Running command: fastANI --query /var/lib/cwl/stgaffc49a4-4454-4700-9024-b3f830382f4b/GCF_003325355.1_ASM332535v1_genomic.fna.gz --refList GCF_003325355.1_ASM332535v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003325355.1_ASM332535v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:37:12,507] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:12,517] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:37:12,517] [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_003325355.1	s__Runella sp003325355	100.0	2379	2384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Runella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003339505.1	s__Runella sp003339505	92.0404	1975	2384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Runella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009905605.1	s__Runella sp009905605	91.8239	1996	2384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Runella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000218895.1	s__Runella slithyformis	81.5771	1409	2384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Runella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003711225.1	s__Runella sp003711225	77.5251	628	2384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Runella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014195535.1	s__Runella defluvii	77.5055	619	2384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Runella	95.0	95.53	95.36	0.92	0.90	3	-
GCF_000974425.1	s__Spirosoma radiotolerans	76.1668	74	2384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Spirosoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004293645.1	s__REAB01 sp004293645	76.1268	217	2384	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__REAB01	95.0	99.03	98.31	0.91	0.83	11	-
--------------------------------------------------------------------------------
[2024-01-24 12:37:12,519] [INFO] GTDB search result was written to GCF_003325355.1_ASM332535v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:37:12,519] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:37:12,522] [INFO] DFAST_QC result json was written to GCF_003325355.1_ASM332535v1_genomic.fna/dqc_result.json
[2024-01-24 12:37:12,522] [INFO] DFAST_QC completed!
[2024-01-24 12:37:12,522] [INFO] Total running time: 0h2m52s