[2024-01-25 18:00:20,828] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:00:20,830] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:00:20,830] [INFO] DQC Reference Directory: /var/lib/cwl/stgee44503b-a90d-4033-878b-d7d97cfca592/dqc_reference
[2024-01-25 18:00:21,938] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:00:21,939] [INFO] Task started: Prodigal
[2024-01-25 18:00:21,939] [INFO] Running command: gunzip -c /var/lib/cwl/stg91b60042-93d0-43f2-a37f-843e30d1a732/GCF_000300005.1_ASM30000v1_genomic.fna.gz | prodigal -d GCF_000300005.1_ASM30000v1_genomic.fna/cds.fna -a GCF_000300005.1_ASM30000v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:00:39,901] [INFO] Task succeeded: Prodigal
[2024-01-25 18:00:39,901] [INFO] Task started: HMMsearch
[2024-01-25 18:00:39,901] [INFO] Running command: hmmsearch --tblout GCF_000300005.1_ASM30000v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee44503b-a90d-4033-878b-d7d97cfca592/dqc_reference/reference_markers.hmm GCF_000300005.1_ASM30000v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:00:40,157] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:00:40,158] [INFO] Found 6/6 markers.
[2024-01-25 18:00:40,195] [INFO] Query marker FASTA was written to GCF_000300005.1_ASM30000v1_genomic.fna/markers.fasta
[2024-01-25 18:00:40,195] [INFO] Task started: Blastn
[2024-01-25 18:00:40,196] [INFO] Running command: blastn -query GCF_000300005.1_ASM30000v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee44503b-a90d-4033-878b-d7d97cfca592/dqc_reference/reference_markers.fasta -out GCF_000300005.1_ASM30000v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:00:41,036] [INFO] Task succeeded: Blastn
[2024-01-25 18:00:41,040] [INFO] Selected 10 target genomes.
[2024-01-25 18:00:41,040] [INFO] Target genome list was writen to GCF_000300005.1_ASM30000v1_genomic.fna/target_genomes.txt
[2024-01-25 18:00:41,047] [INFO] Task started: fastANI
[2024-01-25 18:00:41,048] [INFO] Running command: fastANI --query /var/lib/cwl/stg91b60042-93d0-43f2-a37f-843e30d1a732/GCF_000300005.1_ASM30000v1_genomic.fna.gz --refList GCF_000300005.1_ASM30000v1_genomic.fna/target_genomes.txt --output GCF_000300005.1_ASM30000v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:00:50,229] [INFO] Task succeeded: fastANI
[2024-01-25 18:00:50,230] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee44503b-a90d-4033-878b-d7d97cfca592/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:00:50,230] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee44503b-a90d-4033-878b-d7d97cfca592/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:00:50,237] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 18:00:50,237] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 18:00:50,237] [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
Alcanivorax dieselolei	strain=B5	GCA_000300005.1	285091	285091	type	True	100.0	1641	1642	95	inconclusive
Alcanivorax dieselolei	strain=CGMCC 1.3690	GCA_014644575.1	285091	285091	type	True	99.9861	1610	1642	95	inconclusive
Alcanivorax balearicus	strain=MACL04	GCA_025532145.1	413232	413232	type	True	95.0329	1376	1642	95	inconclusive
Alcanivorax xenomutans	strain=JC109	GCA_900217905.1	1094342	1094342	type	True	93.5366	1296	1642	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	81.1538	706	1642	95	below_threshold
Alcanivorax profundimaris	strain=ST75FaO-1	GCA_015265435.1	2735259	2735259	type	True	81.1181	778	1642	95	below_threshold
Alcanivorax profundi	strain=MTEO17	GCA_003597125.1	2338368	2338368	type	True	78.3947	337	1642	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	77.163	157	1642	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	76.9201	152	1642	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.8837	206	1642	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:00:50,239] [INFO] DFAST Taxonomy check result was written to GCF_000300005.1_ASM30000v1_genomic.fna/tc_result.tsv
[2024-01-25 18:00:50,239] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:00:50,239] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:00:50,239] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee44503b-a90d-4033-878b-d7d97cfca592/dqc_reference/checkm_data
[2024-01-25 18:00:50,240] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:00:50,288] [INFO] Task started: CheckM
[2024-01-25 18:00:50,288] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000300005.1_ASM30000v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000300005.1_ASM30000v1_genomic.fna/checkm_input GCF_000300005.1_ASM30000v1_genomic.fna/checkm_result
[2024-01-25 18:01:46,537] [INFO] Task succeeded: CheckM
[2024-01-25 18:01:46,538] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:01:46,555] [INFO] ===== Completeness check finished =====
[2024-01-25 18:01:46,555] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:01:46,556] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000300005.1_ASM30000v1_genomic.fna/markers.fasta)
[2024-01-25 18:01:46,556] [INFO] Task started: Blastn
[2024-01-25 18:01:46,556] [INFO] Running command: blastn -query GCF_000300005.1_ASM30000v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee44503b-a90d-4033-878b-d7d97cfca592/dqc_reference/reference_markers_gtdb.fasta -out GCF_000300005.1_ASM30000v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:01:48,140] [INFO] Task succeeded: Blastn
[2024-01-25 18:01:48,143] [INFO] Selected 9 target genomes.
[2024-01-25 18:01:48,143] [INFO] Target genome list was writen to GCF_000300005.1_ASM30000v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:01:48,156] [INFO] Task started: fastANI
[2024-01-25 18:01:48,157] [INFO] Running command: fastANI --query /var/lib/cwl/stg91b60042-93d0-43f2-a37f-843e30d1a732/GCF_000300005.1_ASM30000v1_genomic.fna.gz --refList GCF_000300005.1_ASM30000v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000300005.1_ASM30000v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:01:58,108] [INFO] Task succeeded: fastANI
[2024-01-25 18:01:58,115] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:01:58,115] [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_000300005.1	s__Alcanivorax dieselolei	100.0	1639	1642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.56	95.12	0.92	0.84	3	conclusive
GCF_900217905.1	s__Alcanivorax xenomutans	93.5387	1296	1642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.43	98.18	0.92	0.84	9	-
GCF_004360225.1	s__Alcanivorax sp004360225	90.5159	1326	1642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	99.14	99.14	0.91	0.91	2	-
GCF_015265435.1	s__Alcanivorax profundimaris	81.1013	780	1642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.49	97.23	0.85	0.77	11	-
GCF_005938655.1	s__Alcanivorax gelatiniphagus	81.0641	766	1642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.53	98.53	0.93	0.93	3	-
GCA_017794945.1	s__Alcanivorax sp009711585	80.9378	616	1642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	96.99	96.99	0.93	0.93	2	-
GCF_016906305.1	s__Alcanivorax marinus_B	80.9351	786	1642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016785095.1	s__Alcanivorax marinus_A	80.5033	743	1642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762765.1	s__Alcanivorax sp014762765	78.5064	379	1642	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:01:58,116] [INFO] GTDB search result was written to GCF_000300005.1_ASM30000v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:01:58,117] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:01:58,119] [INFO] DFAST_QC result json was written to GCF_000300005.1_ASM30000v1_genomic.fna/dqc_result.json
[2024-01-25 18:01:58,119] [INFO] DFAST_QC completed!
[2024-01-25 18:01:58,119] [INFO] Total running time: 0h1m37s