[2024-01-24 12:15:21,093] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:21,095] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:21,095] [INFO] DQC Reference Directory: /var/lib/cwl/stg28641751-72c5-4656-a46d-d2ba5aba9ad6/dqc_reference
[2024-01-24 12:15:22,471] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:22,479] [INFO] Task started: Prodigal
[2024-01-24 12:15:22,480] [INFO] Running command: gunzip -c /var/lib/cwl/stg114dc2cb-6580-430a-adf7-48fac6d66bf2/GCF_002207865.1_ASM220786v1_genomic.fna.gz | prodigal -d GCF_002207865.1_ASM220786v1_genomic.fna/cds.fna -a GCF_002207865.1_ASM220786v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:30,884] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:30,885] [INFO] Task started: HMMsearch
[2024-01-24 12:15:30,885] [INFO] Running command: hmmsearch --tblout GCF_002207865.1_ASM220786v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg28641751-72c5-4656-a46d-d2ba5aba9ad6/dqc_reference/reference_markers.hmm GCF_002207865.1_ASM220786v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:31,232] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:31,234] [INFO] Found 6/6 markers.
[2024-01-24 12:15:31,280] [INFO] Query marker FASTA was written to GCF_002207865.1_ASM220786v1_genomic.fna/markers.fasta
[2024-01-24 12:15:31,281] [INFO] Task started: Blastn
[2024-01-24 12:15:31,281] [INFO] Running command: blastn -query GCF_002207865.1_ASM220786v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28641751-72c5-4656-a46d-d2ba5aba9ad6/dqc_reference/reference_markers.fasta -out GCF_002207865.1_ASM220786v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:31,998] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:32,018] [INFO] Selected 13 target genomes.
[2024-01-24 12:15:32,019] [INFO] Target genome list was writen to GCF_002207865.1_ASM220786v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:32,025] [INFO] Task started: fastANI
[2024-01-24 12:15:32,026] [INFO] Running command: fastANI --query /var/lib/cwl/stg114dc2cb-6580-430a-adf7-48fac6d66bf2/GCF_002207865.1_ASM220786v1_genomic.fna.gz --refList GCF_002207865.1_ASM220786v1_genomic.fna/target_genomes.txt --output GCF_002207865.1_ASM220786v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:42,278] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:42,279] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg28641751-72c5-4656-a46d-d2ba5aba9ad6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:42,280] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg28641751-72c5-4656-a46d-d2ba5aba9ad6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:42,290] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:42,290] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:42,290] [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
Colwellia marinimaniae	strain=MTCD1	GCA_002207865.1	1513592	1513592	type	True	100.0	1364	1367	95	conclusive
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	82.8288	942	1367	95	below_threshold
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	81.0515	820	1367	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	79.5225	577	1367	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	79.0055	477	1367	95	below_threshold
Litorilituus lipolyticus	strain=RZ04	GCA_006439335.1	2491017	2491017	type	True	78.1806	308	1367	95	below_threshold
Litorilituus sediminis	strain=JCM 17549	GCA_004295665.1	718192	718192	type	True	78.076	343	1367	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:42,292] [INFO] DFAST Taxonomy check result was written to GCF_002207865.1_ASM220786v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:42,292] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:42,293] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:42,293] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg28641751-72c5-4656-a46d-d2ba5aba9ad6/dqc_reference/checkm_data
[2024-01-24 12:15:42,294] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:42,336] [INFO] Task started: CheckM
[2024-01-24 12:15:42,336] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002207865.1_ASM220786v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002207865.1_ASM220786v1_genomic.fna/checkm_input GCF_002207865.1_ASM220786v1_genomic.fna/checkm_result
[2024-01-24 12:16:11,771] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:11,772] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.25%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:11,795] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:11,795] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:11,796] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002207865.1_ASM220786v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:11,796] [INFO] Task started: Blastn
[2024-01-24 12:16:11,796] [INFO] Running command: blastn -query GCF_002207865.1_ASM220786v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg28641751-72c5-4656-a46d-d2ba5aba9ad6/dqc_reference/reference_markers_gtdb.fasta -out GCF_002207865.1_ASM220786v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:12,921] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:12,925] [INFO] Selected 10 target genomes.
[2024-01-24 12:16:12,926] [INFO] Target genome list was writen to GCF_002207865.1_ASM220786v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:12,937] [INFO] Task started: fastANI
[2024-01-24 12:16:12,937] [INFO] Running command: fastANI --query /var/lib/cwl/stg114dc2cb-6580-430a-adf7-48fac6d66bf2/GCF_002207865.1_ASM220786v1_genomic.fna.gz --refList GCF_002207865.1_ASM220786v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002207865.1_ASM220786v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:24,121] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:24,132] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:24,132] [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_002207865.1	s__Colwellia marinimaniae	100.0	1364	1367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	99.40	98.81	0.97	0.94	3	conclusive
GCF_001440345.1	s__Colwellia sp001440345	94.5245	1126	1367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214175.1	s__Colwellia sp013214175	85.1298	1060	1367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	95.17	95.17	0.89	0.89	2	-
GCF_000378625.1	s__Colwellia piezophila	82.8492	940	1367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764185.1	s__Colwellia psychrerythraea_B	81.9914	958	1367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836775.1	s__Colwellia sp002836775	81.1062	849	1367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836255.1	s__Colwellia sp002836255	81.0117	859	1367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012325.1	s__Colwellia psychrerythraea_A	80.8864	809	1367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	98.43	98.43	0.88	0.88	2	-
GCA_013215465.1	s__Colwellia sp013215465	79.3772	421	1367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	96.15	96.15	0.84	0.84	2	-
GCA_002733765.1	s__Colwellia sp002733765	78.9856	349	1367	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	99.46	99.46	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:24,134] [INFO] GTDB search result was written to GCF_002207865.1_ASM220786v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:24,135] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:24,138] [INFO] DFAST_QC result json was written to GCF_002207865.1_ASM220786v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:24,138] [INFO] DFAST_QC completed!
[2024-01-24 12:16:24,138] [INFO] Total running time: 0h1m3s