[2023-06-30 13:24:13,120] [INFO] DFAST_QC pipeline started.
[2023-06-30 13:24:13,123] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 13:24:13,123] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c0e8dfa-0f6e-4ffb-bac4-208e6174464e/dqc_reference
[2023-06-30 13:24:15,000] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 13:24:15,001] [INFO] Task started: Prodigal
[2023-06-30 13:24:15,001] [INFO] Running command: gunzip -c /var/lib/cwl/stg7e1f1d1e-0e3d-44ff-a62c-08cd03eaa929/GCA_900205545.1_PTR11_genomic.fna.gz | prodigal -d GCA_900205545.1_PTR11_genomic.fna/cds.fna -a GCA_900205545.1_PTR11_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 13:24:19,348] [INFO] Task succeeded: Prodigal
[2023-06-30 13:24:19,348] [INFO] Task started: HMMsearch
[2023-06-30 13:24:19,348] [INFO] Running command: hmmsearch --tblout GCA_900205545.1_PTR11_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c0e8dfa-0f6e-4ffb-bac4-208e6174464e/dqc_reference/reference_markers.hmm GCA_900205545.1_PTR11_genomic.fna/protein.faa > /dev/null
[2023-06-30 13:24:19,620] [INFO] Task succeeded: HMMsearch
[2023-06-30 13:24:19,621] [INFO] Found 6/6 markers.
[2023-06-30 13:24:19,646] [INFO] Query marker FASTA was written to GCA_900205545.1_PTR11_genomic.fna/markers.fasta
[2023-06-30 13:24:19,646] [INFO] Task started: Blastn
[2023-06-30 13:24:19,646] [INFO] Running command: blastn -query GCA_900205545.1_PTR11_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c0e8dfa-0f6e-4ffb-bac4-208e6174464e/dqc_reference/reference_markers.fasta -out GCA_900205545.1_PTR11_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 13:24:20,335] [INFO] Task succeeded: Blastn
[2023-06-30 13:24:20,339] [INFO] Selected 18 target genomes.
[2023-06-30 13:24:20,340] [INFO] Target genome list was writen to GCA_900205545.1_PTR11_genomic.fna/target_genomes.txt
[2023-06-30 13:24:20,342] [INFO] Task started: fastANI
[2023-06-30 13:24:20,343] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e1f1d1e-0e3d-44ff-a62c-08cd03eaa929/GCA_900205545.1_PTR11_genomic.fna.gz --refList GCA_900205545.1_PTR11_genomic.fna/target_genomes.txt --output GCA_900205545.1_PTR11_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 13:24:32,973] [INFO] Task succeeded: fastANI
[2023-06-30 13:24:32,973] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c0e8dfa-0f6e-4ffb-bac4-208e6174464e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 13:24:32,973] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c0e8dfa-0f6e-4ffb-bac4-208e6174464e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 13:24:32,991] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 13:24:32,992] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 13:24:32,992] [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 demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	79.7221	331	796	95	below_threshold
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	78.6767	268	796	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	78.6681	280	796	95	below_threshold
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	78.6006	210	796	95	below_threshold
Colwellia marinimaniae	strain=MTCD1	GCA_002207865.1	1513592	1513592	type	True	78.5497	264	796	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	78.2442	293	796	95	below_threshold
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	78.1093	201	796	95	below_threshold
Litorilituus lipolyticus	strain=RZ04	GCA_006439335.1	2491017	2491017	type	True	77.9647	225	796	95	below_threshold
Thalassotalea algicola	strain=M1531	GCA_012932965.1	2716224	2716224	type	True	77.8465	121	796	95	below_threshold
Thalassotalea marina	strain=KCTC 42731	GCA_014656435.1	1673741	1673741	type	True	77.0905	115	796	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	75.8845	63	796	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 13:24:32,995] [INFO] DFAST Taxonomy check result was written to GCA_900205545.1_PTR11_genomic.fna/tc_result.tsv
[2023-06-30 13:24:32,996] [INFO] ===== Taxonomy check completed =====
[2023-06-30 13:24:32,996] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 13:24:32,996] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c0e8dfa-0f6e-4ffb-bac4-208e6174464e/dqc_reference/checkm_data
[2023-06-30 13:24:32,998] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 13:24:33,028] [INFO] Task started: CheckM
[2023-06-30 13:24:33,028] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900205545.1_PTR11_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900205545.1_PTR11_genomic.fna/checkm_input GCA_900205545.1_PTR11_genomic.fna/checkm_result
[2023-06-30 13:24:54,116] [INFO] Task succeeded: CheckM
[2023-06-30 13:24:54,117] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.36%
Contamintation: 8.75%
Strain heterogeneity: 87.50%
--------------------------------------------------------------------------------
[2023-06-30 13:24:54,142] [INFO] ===== Completeness check finished =====
[2023-06-30 13:24:54,142] [INFO] ===== Start GTDB Search =====
[2023-06-30 13:24:54,142] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900205545.1_PTR11_genomic.fna/markers.fasta)
[2023-06-30 13:24:54,143] [INFO] Task started: Blastn
[2023-06-30 13:24:54,143] [INFO] Running command: blastn -query GCA_900205545.1_PTR11_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c0e8dfa-0f6e-4ffb-bac4-208e6174464e/dqc_reference/reference_markers_gtdb.fasta -out GCA_900205545.1_PTR11_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 13:24:55,213] [INFO] Task succeeded: Blastn
[2023-06-30 13:24:55,217] [INFO] Selected 11 target genomes.
[2023-06-30 13:24:55,218] [INFO] Target genome list was writen to GCA_900205545.1_PTR11_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 13:24:55,223] [INFO] Task started: fastANI
[2023-06-30 13:24:55,224] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e1f1d1e-0e3d-44ff-a62c-08cd03eaa929/GCA_900205545.1_PTR11_genomic.fna.gz --refList GCA_900205545.1_PTR11_genomic.fna/target_genomes_gtdb.txt --output GCA_900205545.1_PTR11_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 13:25:03,828] [INFO] Task succeeded: fastANI
[2023-06-30 13:25:03,841] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 13:25:03,842] [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
GCA_003521815.1	s__Colwellia sp003521815	94.6398	636	796	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003333305.1	s__Colwellia aromaticivorans	86.2859	634	796	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733765.1	s__Colwellia sp002733765	84.881	629	796	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	99.46	99.46	0.95	0.95	2	-
GCA_013215465.1	s__Colwellia sp013215465	84.0343	623	796	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	96.15	96.15	0.84	0.84	2	-
GCF_000012325.1	s__Colwellia psychrerythraea_A	79.7516	317	796	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	98.43	98.43	0.88	0.88	2	-
GCF_007954275.1	s__Colwellia demingiae	79.7265	330	796	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016745015.1	s__Colwellia sp016745015	79.6072	369	796	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002163005.1	s__Colwellia psychrerythraea_C	79.2595	304	796	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	79.2001	309	796	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016765685.1	s__Colwellia sp016765685	78.6991	253	796	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005885605.1	s__Colwellia ponticola	78.6541	280	796	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 13:25:03,844] [INFO] GTDB search result was written to GCA_900205545.1_PTR11_genomic.fna/result_gtdb.tsv
[2023-06-30 13:25:03,845] [INFO] ===== GTDB Search completed =====
[2023-06-30 13:25:03,851] [INFO] DFAST_QC result json was written to GCA_900205545.1_PTR11_genomic.fna/dqc_result.json
[2023-06-30 13:25:03,851] [INFO] DFAST_QC completed!
[2023-06-30 13:25:03,852] [INFO] Total running time: 0h0m51s