[2024-01-24 11:05:03,934] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:03,936] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:03,937] [INFO] DQC Reference Directory: /var/lib/cwl/stg589e0d91-334e-47f8-a96e-01cd6ff906a4/dqc_reference
[2024-01-24 11:05:05,814] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:05,815] [INFO] Task started: Prodigal
[2024-01-24 11:05:05,815] [INFO] Running command: gunzip -c /var/lib/cwl/stg8c0abfca-9386-4fd4-8196-10a07db64316/GCF_009183365.2_ASM918336v2_genomic.fna.gz | prodigal -d GCF_009183365.2_ASM918336v2_genomic.fna/cds.fna -a GCF_009183365.2_ASM918336v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:18,721] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:18,722] [INFO] Task started: HMMsearch
[2024-01-24 11:05:18,722] [INFO] Running command: hmmsearch --tblout GCF_009183365.2_ASM918336v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg589e0d91-334e-47f8-a96e-01cd6ff906a4/dqc_reference/reference_markers.hmm GCF_009183365.2_ASM918336v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:19,007] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:19,010] [INFO] Found 6/6 markers.
[2024-01-24 11:05:19,049] [INFO] Query marker FASTA was written to GCF_009183365.2_ASM918336v2_genomic.fna/markers.fasta
[2024-01-24 11:05:19,050] [INFO] Task started: Blastn
[2024-01-24 11:05:19,050] [INFO] Running command: blastn -query GCF_009183365.2_ASM918336v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg589e0d91-334e-47f8-a96e-01cd6ff906a4/dqc_reference/reference_markers.fasta -out GCF_009183365.2_ASM918336v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:19,905] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:19,907] [INFO] Selected 13 target genomes.
[2024-01-24 11:05:19,908] [INFO] Target genome list was writen to GCF_009183365.2_ASM918336v2_genomic.fna/target_genomes.txt
[2024-01-24 11:05:19,911] [INFO] Task started: fastANI
[2024-01-24 11:05:19,912] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c0abfca-9386-4fd4-8196-10a07db64316/GCF_009183365.2_ASM918336v2_genomic.fna.gz --refList GCF_009183365.2_ASM918336v2_genomic.fna/target_genomes.txt --output GCF_009183365.2_ASM918336v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:05:34,676] [INFO] Task succeeded: fastANI
[2024-01-24 11:05:34,677] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg589e0d91-334e-47f8-a96e-01cd6ff906a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:05:34,677] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg589e0d91-334e-47f8-a96e-01cd6ff906a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:05:34,686] [INFO] Found 13 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:05:34,686] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:05:34,686] [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
Shewanella algae	strain=CECT 5071	GCA_009183365.2	38313	38313	type	True	100.0	1641	1641	95	conclusive
Shewanella algae	strain=ATCC 51192	GCA_012396675.1	38313	38313	type	True	99.979	1603	1641	95	conclusive
Shewanella algae	strain=NBRC 103173	GCA_001598875.1	38313	38313	type	True	99.9362	1527	1641	95	conclusive
Shewanella chilikensis	strain=KCTC 22540	GCA_014651975.1	558541	558541	type	True	94.3663	1318	1641	95	below_threshold
Shewanella chilikensis	strain=CCUG 57101	GCA_023283475.1	558541	558541	type	True	94.345	1337	1641	95	below_threshold
Shewanella chilikensis	strain=JC5	GCA_003217175.1	558541	558541	type	True	94.336	1332	1641	95	below_threshold
Shewanella indica	strain=KJW27	GCA_002836975.1	768528	768528	type	True	94.1427	1320	1641	95	below_threshold
Shewanella carassii	strain=CGMCC 1.16033	GCA_014644375.1	1987584	1987584	type	True	93.8136	1334	1641	95	below_threshold
Shewanella carassii	strain=08MAS2251	GCA_002777975.1	1987584	1987584	type	True	93.7802	1340	1641	95	below_threshold
Shewanella litorisediminis	strain=CCUG 62411	GCA_023349165.1	1173586	1173586	type	True	78.7294	423	1641	95	below_threshold
Shewanella aquimarina	strain=JCM 12193	GCA_023349185.1	260365	260365	type	True	78.1511	397	1641	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	77.6802	51	1641	95	below_threshold
Oceanobacter mangrovi	strain=SM2-42	GCA_019740315.1	2862510	2862510	type	True	76.3186	58	1641	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:05:34,688] [INFO] DFAST Taxonomy check result was written to GCF_009183365.2_ASM918336v2_genomic.fna/tc_result.tsv
[2024-01-24 11:05:34,688] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:05:34,688] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:05:34,688] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg589e0d91-334e-47f8-a96e-01cd6ff906a4/dqc_reference/checkm_data
[2024-01-24 11:05:34,689] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:05:34,737] [INFO] Task started: CheckM
[2024-01-24 11:05:34,737] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009183365.2_ASM918336v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009183365.2_ASM918336v2_genomic.fna/checkm_input GCF_009183365.2_ASM918336v2_genomic.fna/checkm_result
[2024-01-24 11:06:13,920] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:13,921] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:13,936] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:13,936] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:13,936] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009183365.2_ASM918336v2_genomic.fna/markers.fasta)
[2024-01-24 11:06:13,936] [INFO] Task started: Blastn
[2024-01-24 11:06:13,936] [INFO] Running command: blastn -query GCF_009183365.2_ASM918336v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg589e0d91-334e-47f8-a96e-01cd6ff906a4/dqc_reference/reference_markers_gtdb.fasta -out GCF_009183365.2_ASM918336v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:15,228] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:15,230] [INFO] Selected 8 target genomes.
[2024-01-24 11:06:15,230] [INFO] Target genome list was writen to GCF_009183365.2_ASM918336v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:15,235] [INFO] Task started: fastANI
[2024-01-24 11:06:15,235] [INFO] Running command: fastANI --query /var/lib/cwl/stg8c0abfca-9386-4fd4-8196-10a07db64316/GCF_009183365.2_ASM918336v2_genomic.fna.gz --refList GCF_009183365.2_ASM918336v2_genomic.fna/target_genomes_gtdb.txt --output GCF_009183365.2_ASM918336v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:06:24,529] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:24,535] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:06:24,535] [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_009183365.2	s__Shewanella algae	100.0	1641	1641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.21	97.66	0.95	0.92	87	conclusive
GCF_002836945.1	s__Shewanella chilikensis	94.3451	1317	1641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.7827	99.40	98.79	0.97	0.93	5	-
GCF_002836975.1	s__Shewanella indica	94.1186	1322	1641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.7827	98.42	98.01	0.95	0.93	6	-
GCF_002777975.1	s__Shewanella carassii	93.7756	1341	1641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_017354985.1	s__Shewanella sp017354985	79.4848	488	1641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.75	95.81	0.93	0.92	3	-
GCF_000015245.1	s__Shewanella amazonensis	79.1359	436	1641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003353085.1	s__Shewanella corallii	78.7816	318	1641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012911865.1	s__Shewanella sp012911865	78.5529	432	1641	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:06:24,536] [INFO] GTDB search result was written to GCF_009183365.2_ASM918336v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:06:24,537] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:06:24,539] [INFO] DFAST_QC result json was written to GCF_009183365.2_ASM918336v2_genomic.fna/dqc_result.json
[2024-01-24 11:06:24,540] [INFO] DFAST_QC completed!
[2024-01-24 11:06:24,540] [INFO] Total running time: 0h1m21s