[2023-03-17 07:44:36,993] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:44:36,993] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:44:36,993] [INFO] DQC Reference Directory: /var/lib/cwl/stg4c320659-2f81-47d1-b088-01a7efd4dbe2/dqc_reference
[2023-03-17 07:44:38,849] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:44:38,850] [INFO] Task started: Prodigal
[2023-03-17 07:44:38,850] [INFO] Running command: cat /var/lib/cwl/stg32e673e2-ee17-46ef-95da-1cacefaab4f9/OceanDNA-b35228.fa | prodigal -d OceanDNA-b35228/cds.fna -a OceanDNA-b35228/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:44:59,944] [INFO] Task succeeded: Prodigal
[2023-03-17 07:44:59,945] [INFO] Task started: HMMsearch
[2023-03-17 07:44:59,945] [INFO] Running command: hmmsearch --tblout OceanDNA-b35228/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4c320659-2f81-47d1-b088-01a7efd4dbe2/dqc_reference/reference_markers.hmm OceanDNA-b35228/protein.faa > /dev/null
[2023-03-17 07:45:00,176] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:45:00,176] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg32e673e2-ee17-46ef-95da-1cacefaab4f9/OceanDNA-b35228.fa]
[2023-03-17 07:45:00,198] [INFO] Query marker FASTA was written to OceanDNA-b35228/markers.fasta
[2023-03-17 07:45:00,198] [INFO] Task started: Blastn
[2023-03-17 07:45:00,198] [INFO] Running command: blastn -query OceanDNA-b35228/markers.fasta -db /var/lib/cwl/stg4c320659-2f81-47d1-b088-01a7efd4dbe2/dqc_reference/reference_markers.fasta -out OceanDNA-b35228/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:45:00,839] [INFO] Task succeeded: Blastn
[2023-03-17 07:45:00,840] [INFO] Selected 20 target genomes.
[2023-03-17 07:45:00,840] [INFO] Target genome list was writen to OceanDNA-b35228/target_genomes.txt
[2023-03-17 07:45:00,900] [INFO] Task started: fastANI
[2023-03-17 07:45:00,900] [INFO] Running command: fastANI --query /var/lib/cwl/stg32e673e2-ee17-46ef-95da-1cacefaab4f9/OceanDNA-b35228.fa --refList OceanDNA-b35228/target_genomes.txt --output OceanDNA-b35228/fastani_result.tsv --threads 1
[2023-03-17 07:45:15,289] [INFO] Task succeeded: fastANI
[2023-03-17 07:45:15,289] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4c320659-2f81-47d1-b088-01a7efd4dbe2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:45:15,290] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4c320659-2f81-47d1-b088-01a7efd4dbe2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:45:15,297] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:45:15,297] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 07:45:15,297] [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
Psychromonas hadalis	strain=ATCC BAA-638	GCA_000420245.1	211669	211669	type	True	78.8774	385	1324	95	below_threshold
Psychromonas arctica	strain=DSM 14288	GCA_000482725.1	168275	168275	type	True	78.498	290	1324	95	below_threshold
Psychromonas ossibalaenae	strain=JAMM 0738	GCA_000381745.1	444922	444922	type	True	77.9732	229	1324	95	below_threshold
Psychromonas aquimarina	strain=ATCC BAA-1526	GCA_000428725.1	444919	444919	type	True	77.9499	219	1324	95	below_threshold
Psychromonas antarctica	strain=DSM 10704	GCA_022267535.1	67573	67573	type	True	77.8273	234	1324	95	below_threshold
Motilimonas cestriensis	strain=MKS20	GCA_021295315.1	2742685	2742685	type	True	76.5121	76	1324	95	below_threshold
Moritella dasanensis	strain=ArB 0140	GCA_000276805.1	428031	428031	type	True	76.4364	70	1324	95	below_threshold
Pseudoalteromonas fuliginea	strain=KMM 216	GCA_000690055.1	1872678	1872678	type	True	76.0136	52	1324	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	76.0096	72	1324	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	75.9448	55	1324	95	below_threshold
Pseudoalteromonas nigrifaciens	strain=NCTC10691	GCA_900455185.1	28109	28109	type	True	75.6672	50	1324	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 07:45:15,297] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35228/tc_result.tsv
[2023-03-17 07:45:15,298] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:45:15,298] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:45:15,298] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4c320659-2f81-47d1-b088-01a7efd4dbe2/dqc_reference/checkm_data
[2023-03-17 07:45:15,298] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:45:15,305] [INFO] Task started: CheckM
[2023-03-17 07:45:15,305] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35228/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35228/checkm_input OceanDNA-b35228/checkm_result
[2023-03-17 07:46:08,299] [INFO] Task succeeded: CheckM
[2023-03-17 07:46:08,299] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 65.15%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:46:08,302] [INFO] ===== Completeness check finished =====
[2023-03-17 07:46:08,302] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:46:08,302] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35228/markers.fasta)
[2023-03-17 07:46:08,303] [INFO] Task started: Blastn
[2023-03-17 07:46:08,303] [INFO] Running command: blastn -query OceanDNA-b35228/markers.fasta -db /var/lib/cwl/stg4c320659-2f81-47d1-b088-01a7efd4dbe2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35228/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:46:09,306] [INFO] Task succeeded: Blastn
[2023-03-17 07:46:09,307] [INFO] Selected 15 target genomes.
[2023-03-17 07:46:09,307] [INFO] Target genome list was writen to OceanDNA-b35228/target_genomes_gtdb.txt
[2023-03-17 07:46:09,326] [INFO] Task started: fastANI
[2023-03-17 07:46:09,327] [INFO] Running command: fastANI --query /var/lib/cwl/stg32e673e2-ee17-46ef-95da-1cacefaab4f9/OceanDNA-b35228.fa --refList OceanDNA-b35228/target_genomes_gtdb.txt --output OceanDNA-b35228/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:46:20,937] [INFO] Task succeeded: fastANI
[2023-03-17 07:46:20,946] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 07:46:20,946] [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_002835995.1	s__Psychromonas sp002835995	80.0792	533	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002835465.1	s__Psychromonas sp002835465	79.1703	405	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420245.1	s__Psychromonas hadalis	78.8694	385	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004378355.1	s__Psychromonas sp004378355	78.7728	273	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004376845.1	s__Psychromonas sp004376845	78.6252	268	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011378715.1	s__Psychromonas sp011378715	78.5622	294	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000482725.1	s__Psychromonas arctica	78.4692	292	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	98.18	98.18	0.89	0.89	2	-
GCF_009828855.1	s__Psychromonas sp009828855	78.4017	309	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	98.96	98.96	0.95	0.95	2	-
GCF_000470315.2	s__Psychromonas sp000470315	78.2917	310	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003318165.1	s__Psychromonas sp003318165	78.2888	237	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153405.2	s__Psychromonas sp000153405	78.2264	186	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013619145.1	s__Psychromonas sp013619145	78.1488	258	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381745.1	s__Psychromonas ossibalaenae	78.0046	227	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428725.1	s__Psychromonas aquimarina	77.9784	218	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000690055.1	s__Pseudoalteromonas fuliginea	76.0506	51	1324	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.33	97.88	0.92	0.87	9	-
--------------------------------------------------------------------------------
[2023-03-17 07:46:20,946] [INFO] GTDB search result was written to OceanDNA-b35228/result_gtdb.tsv
[2023-03-17 07:46:20,947] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:46:20,948] [INFO] DFAST_QC result json was written to OceanDNA-b35228/dqc_result.json
[2023-03-17 07:46:20,948] [INFO] DFAST_QC completed!
[2023-03-17 07:46:20,948] [INFO] Total running time: 0h1m44s