[2024-01-24 15:18:21,996] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:21,997] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:21,998] [INFO] DQC Reference Directory: /var/lib/cwl/stg746aef32-c0f9-4e8c-97e7-b522da92951c/dqc_reference
[2024-01-24 15:18:25,004] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:25,005] [INFO] Task started: Prodigal
[2024-01-24 15:18:25,005] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf398fbe-6fae-4a30-bd33-e61a5e4dfa85/GCF_015265435.1_ASM1526543v1_genomic.fna.gz | prodigal -d GCF_015265435.1_ASM1526543v1_genomic.fna/cds.fna -a GCF_015265435.1_ASM1526543v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:38,360] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:38,360] [INFO] Task started: HMMsearch
[2024-01-24 15:18:38,360] [INFO] Running command: hmmsearch --tblout GCF_015265435.1_ASM1526543v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg746aef32-c0f9-4e8c-97e7-b522da92951c/dqc_reference/reference_markers.hmm GCF_015265435.1_ASM1526543v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:38,752] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:38,754] [INFO] Found 6/6 markers.
[2024-01-24 15:18:38,798] [INFO] Query marker FASTA was written to GCF_015265435.1_ASM1526543v1_genomic.fna/markers.fasta
[2024-01-24 15:18:38,799] [INFO] Task started: Blastn
[2024-01-24 15:18:38,799] [INFO] Running command: blastn -query GCF_015265435.1_ASM1526543v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg746aef32-c0f9-4e8c-97e7-b522da92951c/dqc_reference/reference_markers.fasta -out GCF_015265435.1_ASM1526543v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:39,922] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:39,964] [INFO] Selected 11 target genomes.
[2024-01-24 15:18:39,965] [INFO] Target genome list was writen to GCF_015265435.1_ASM1526543v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:39,970] [INFO] Task started: fastANI
[2024-01-24 15:18:39,970] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf398fbe-6fae-4a30-bd33-e61a5e4dfa85/GCF_015265435.1_ASM1526543v1_genomic.fna.gz --refList GCF_015265435.1_ASM1526543v1_genomic.fna/target_genomes.txt --output GCF_015265435.1_ASM1526543v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:51,105] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:51,105] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg746aef32-c0f9-4e8c-97e7-b522da92951c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:51,106] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg746aef32-c0f9-4e8c-97e7-b522da92951c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:51,120] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:18:51,120] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:51,120] [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 profundimaris	strain=ST75FaO-1	GCA_015265435.1	2735259	2735259	type	True	100.0	1326	1328	95	conclusive
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	88.4236	945	1328	95	below_threshold
Alcanivorax gelatiniphagus	strain=MEBiC 08158	GCA_005938655.1	1194167	1194167	type	True	87.9919	1069	1328	95	below_threshold
Alcanivorax venustensis	strain=ISO4	GCA_015356855.1	172371	172371	type	True	85.68	888	1328	95	below_threshold
Alcanivorax mobilis	strain=MT13131	GCA_002864685.1	2019569	2019569	type	True	82.4956	824	1328	95	below_threshold
Alcanivorax dieselolei	strain=CGMCC 1.3690	GCA_014644575.1	285091	285091	type	True	81.1608	776	1328	95	below_threshold
Alcanivorax balearicus	strain=MACL04	GCA_025532145.1	413232	413232	type	True	80.9061	722	1328	95	below_threshold
Alcanivorax xenomutans	strain=JC109	GCA_900217905.1	1094342	1094342	type	True	80.7351	720	1328	95	below_threshold
Alcanivorax limicola	strain=JB21	GCA_019931215.1	2874102	2874102	type	True	78.0943	337	1328	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	77.7727	334	1328	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	77.6571	355	1328	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:51,122] [INFO] DFAST Taxonomy check result was written to GCF_015265435.1_ASM1526543v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:51,123] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:51,123] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:51,123] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg746aef32-c0f9-4e8c-97e7-b522da92951c/dqc_reference/checkm_data
[2024-01-24 15:18:51,124] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:51,171] [INFO] Task started: CheckM
[2024-01-24 15:18:51,172] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015265435.1_ASM1526543v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015265435.1_ASM1526543v1_genomic.fna/checkm_input GCF_015265435.1_ASM1526543v1_genomic.fna/checkm_result
[2024-01-24 15:19:31,265] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:31,267] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:31,288] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:31,289] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:31,289] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015265435.1_ASM1526543v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:31,290] [INFO] Task started: Blastn
[2024-01-24 15:19:31,290] [INFO] Running command: blastn -query GCF_015265435.1_ASM1526543v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg746aef32-c0f9-4e8c-97e7-b522da92951c/dqc_reference/reference_markers_gtdb.fasta -out GCF_015265435.1_ASM1526543v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:33,130] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:33,133] [INFO] Selected 8 target genomes.
[2024-01-24 15:19:33,133] [INFO] Target genome list was writen to GCF_015265435.1_ASM1526543v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:33,140] [INFO] Task started: fastANI
[2024-01-24 15:19:33,141] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf398fbe-6fae-4a30-bd33-e61a5e4dfa85/GCF_015265435.1_ASM1526543v1_genomic.fna.gz --refList GCF_015265435.1_ASM1526543v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015265435.1_ASM1526543v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:42,041] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:42,053] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:42,053] [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_015265435.1	s__Alcanivorax profundimaris	100.0	1326	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.49	97.23	0.85	0.77	11	conclusive
GCF_016785095.1	s__Alcanivorax marinus_A	91.3617	1129	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016906305.1	s__Alcanivorax marinus_B	88.3497	1062	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938655.1	s__Alcanivorax gelatiniphagus	88.0176	1067	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.53	98.53	0.93	0.93	3	-
GCF_015356855.1	s__Alcanivorax venustensis	85.6821	888	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.73	95.38	0.91	0.87	46	-
GCA_017794945.1	s__Alcanivorax sp009711585	85.295	812	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	96.99	96.99	0.93	0.93	2	-
GCA_002389055.1	s__Alcanivorax sp002389055	84.2207	777	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	96.98	96.27	0.78	0.74	3	-
GCF_004360225.1	s__Alcanivorax sp004360225	80.6559	701	1328	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	99.14	99.14	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:42,054] [INFO] GTDB search result was written to GCF_015265435.1_ASM1526543v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:42,055] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:42,058] [INFO] DFAST_QC result json was written to GCF_015265435.1_ASM1526543v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:42,059] [INFO] DFAST_QC completed!
[2024-01-24 15:19:42,059] [INFO] Total running time: 0h1m20s