[2023-03-18 01:08:39,310] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:08:39,310] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:08:39,310] [INFO] DQC Reference Directory: /var/lib/cwl/stgd12918d5-03fd-40b0-a065-83e1d0880818/dqc_reference
[2023-03-18 01:08:40,450] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:08:40,450] [INFO] Task started: Prodigal
[2023-03-18 01:08:40,450] [INFO] Running command: cat /var/lib/cwl/stg6b102589-d78c-4427-92bd-ef0d160854a4/OceanDNA-b34981.fa | prodigal -d OceanDNA-b34981/cds.fna -a OceanDNA-b34981/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:08:59,740] [INFO] Task succeeded: Prodigal
[2023-03-18 01:08:59,740] [INFO] Task started: HMMsearch
[2023-03-18 01:08:59,740] [INFO] Running command: hmmsearch --tblout OceanDNA-b34981/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd12918d5-03fd-40b0-a065-83e1d0880818/dqc_reference/reference_markers.hmm OceanDNA-b34981/protein.faa > /dev/null
[2023-03-18 01:08:59,976] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:08:59,977] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg6b102589-d78c-4427-92bd-ef0d160854a4/OceanDNA-b34981.fa]
[2023-03-18 01:09:00,006] [INFO] Query marker FASTA was written to OceanDNA-b34981/markers.fasta
[2023-03-18 01:09:00,007] [INFO] Task started: Blastn
[2023-03-18 01:09:00,007] [INFO] Running command: blastn -query OceanDNA-b34981/markers.fasta -db /var/lib/cwl/stgd12918d5-03fd-40b0-a065-83e1d0880818/dqc_reference/reference_markers.fasta -out OceanDNA-b34981/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:09:00,563] [INFO] Task succeeded: Blastn
[2023-03-18 01:09:00,566] [INFO] Selected 12 target genomes.
[2023-03-18 01:09:00,566] [INFO] Target genome list was writen to OceanDNA-b34981/target_genomes.txt
[2023-03-18 01:09:00,575] [INFO] Task started: fastANI
[2023-03-18 01:09:00,575] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b102589-d78c-4427-92bd-ef0d160854a4/OceanDNA-b34981.fa --refList OceanDNA-b34981/target_genomes.txt --output OceanDNA-b34981/fastani_result.tsv --threads 1
[2023-03-18 01:09:13,309] [INFO] Task succeeded: fastANI
[2023-03-18 01:09:13,310] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd12918d5-03fd-40b0-a065-83e1d0880818/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:09:13,310] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd12918d5-03fd-40b0-a065-83e1d0880818/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:09:13,317] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 01:09:13,317] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 01:09:13,317] [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
Pseudoalteromonas aliena	strain=SW19	GCA_014905615.1	247523	247523	type	True	98.7812	1162	1228	95	conclusive
Pseudoalteromonas fuliginea	strain=KMM 216	GCA_000690055.1	1872678	1872678	type	True	87.4902	896	1228	95	below_threshold
Pseudoalteromonas arctica	strain=A 37-1-2	GCA_000238395.4	394751	394751	type	True	87.0213	861	1228	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	86.5848	843	1228	95	below_threshold
Pseudoalteromonas nigrifaciens	strain=NBRC 103036	GCA_007991255.1	28109	28109	type	True	81.8479	657	1228	95	below_threshold
Pseudoalteromonas nigrifaciens	strain=KMM 661	GCA_002221505.1	28109	28109	type	True	81.7728	670	1228	95	below_threshold
Pseudoalteromonas nigrifaciens	strain=NCTC10691	GCA_900455185.1	28109	28109	type	True	81.7384	674	1228	95	below_threshold
Pseudoalteromonas translucida	strain=KMM 520	GCA_001465295.1	166935	166935	type	True	81.7338	679	1228	95	below_threshold
Shewanella electrodiphila	strain=DSM 24955	GCA_023283985.1	934143	934143	type	True	76.1899	54	1228	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:09:13,320] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34981/tc_result.tsv
[2023-03-18 01:09:13,320] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:09:13,320] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:09:13,320] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd12918d5-03fd-40b0-a065-83e1d0880818/dqc_reference/checkm_data
[2023-03-18 01:09:13,321] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:09:13,330] [INFO] Task started: CheckM
[2023-03-18 01:09:13,330] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34981/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34981/checkm_input OceanDNA-b34981/checkm_result
[2023-03-18 01:10:02,316] [INFO] Task succeeded: CheckM
[2023-03-18 01:10:02,316] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 40.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:10:02,322] [INFO] ===== Completeness check finished =====
[2023-03-18 01:10:02,322] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:10:02,322] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34981/markers.fasta)
[2023-03-18 01:10:02,323] [INFO] Task started: Blastn
[2023-03-18 01:10:02,323] [INFO] Running command: blastn -query OceanDNA-b34981/markers.fasta -db /var/lib/cwl/stgd12918d5-03fd-40b0-a065-83e1d0880818/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34981/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:10:03,121] [INFO] Task succeeded: Blastn
[2023-03-18 01:10:03,122] [INFO] Selected 9 target genomes.
[2023-03-18 01:10:03,123] [INFO] Target genome list was writen to OceanDNA-b34981/target_genomes_gtdb.txt
[2023-03-18 01:10:03,133] [INFO] Task started: fastANI
[2023-03-18 01:10:03,133] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b102589-d78c-4427-92bd-ef0d160854a4/OceanDNA-b34981.fa --refList OceanDNA-b34981/target_genomes_gtdb.txt --output OceanDNA-b34981/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:10:15,593] [INFO] Task succeeded: fastANI
[2023-03-18 01:10:15,599] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:10:15,599] [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_014905615.1	s__Pseudoalteromonas aliena	98.7908	1162	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.51	97.10	0.91	0.88	7	conclusive
GCF_000690055.1	s__Pseudoalteromonas fuliginea	87.4562	898	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.33	97.88	0.92	0.87	9	-
GCF_000238395.3	s__Pseudoalteromonas arctica	87.0296	860	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.91	96.03	0.87	0.80	33	-
GCA_000814675.1	s__Pseudoalteromonas distincta	86.6223	841	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.26	95.34	0.88	0.77	38	-
GCF_001974875.1	s__Pseudoalteromonas sp001974875	86.5978	874	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.73	97.18	0.90	0.86	5	-
GCF_011378855.1	s__Pseudoalteromonas sp011378855	86.4614	833	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.10	97.06	0.91	0.90	3	-
GCF_000239855.1	s__Pseudoalteromonas sp000239855	86.2845	796	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008370255.1	s__Pseudoalteromonas sp008370255	86.2635	850	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000498095.1	s__Pseudoalteromonas sp000498095	85.2561	803	1228	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.86	97.76	0.88	0.87	3	-
--------------------------------------------------------------------------------
[2023-03-18 01:10:15,599] [INFO] GTDB search result was written to OceanDNA-b34981/result_gtdb.tsv
[2023-03-18 01:10:15,600] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:10:15,601] [INFO] DFAST_QC result json was written to OceanDNA-b34981/dqc_result.json
[2023-03-18 01:10:15,601] [INFO] DFAST_QC completed!
[2023-03-18 01:10:15,601] [INFO] Total running time: 0h1m36s