[2023-03-18 03:09:35,420] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:09:35,420] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:09:35,420] [INFO] DQC Reference Directory: /var/lib/cwl/stg236dddcf-794f-43b8-84c6-878b44a70dd1/dqc_reference
[2023-03-18 03:09:36,682] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:09:36,682] [INFO] Task started: Prodigal
[2023-03-18 03:09:36,682] [INFO] Running command: cat /var/lib/cwl/stg5e2517db-afc5-4343-9b91-3ff7318e90c5/OceanDNA-b38962.fa | prodigal -d OceanDNA-b38962/cds.fna -a OceanDNA-b38962/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:09:46,182] [INFO] Task succeeded: Prodigal
[2023-03-18 03:09:46,182] [INFO] Task started: HMMsearch
[2023-03-18 03:09:46,182] [INFO] Running command: hmmsearch --tblout OceanDNA-b38962/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg236dddcf-794f-43b8-84c6-878b44a70dd1/dqc_reference/reference_markers.hmm OceanDNA-b38962/protein.faa > /dev/null
[2023-03-18 03:09:46,518] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:09:46,519] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5e2517db-afc5-4343-9b91-3ff7318e90c5/OceanDNA-b38962.fa]
[2023-03-18 03:09:46,536] [INFO] Query marker FASTA was written to OceanDNA-b38962/markers.fasta
[2023-03-18 03:09:46,536] [INFO] Task started: Blastn
[2023-03-18 03:09:46,537] [INFO] Running command: blastn -query OceanDNA-b38962/markers.fasta -db /var/lib/cwl/stg236dddcf-794f-43b8-84c6-878b44a70dd1/dqc_reference/reference_markers.fasta -out OceanDNA-b38962/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:09:47,161] [INFO] Task succeeded: Blastn
[2023-03-18 03:09:47,162] [INFO] Selected 15 target genomes.
[2023-03-18 03:09:47,163] [INFO] Target genome list was writen to OceanDNA-b38962/target_genomes.txt
[2023-03-18 03:09:47,172] [INFO] Task started: fastANI
[2023-03-18 03:09:47,172] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e2517db-afc5-4343-9b91-3ff7318e90c5/OceanDNA-b38962.fa --refList OceanDNA-b38962/target_genomes.txt --output OceanDNA-b38962/fastani_result.tsv --threads 1
[2023-03-18 03:09:56,357] [INFO] Task succeeded: fastANI
[2023-03-18 03:09:56,357] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg236dddcf-794f-43b8-84c6-878b44a70dd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:09:56,357] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg236dddcf-794f-43b8-84c6-878b44a70dd1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:09:56,366] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:09:56,366] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 03:09:56,366] [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
Marinobacter salexigens	strain=HJR7	GCA_002806945.1	1925763	1925763	type	True	80.6998	323	460	95	below_threshold
Marinobacter maritimus	strain=CK47	GCA_007671675.1	277961	277961	type	True	80.4758	331	460	95	below_threshold
Marinobacter antarcticus	strain=CGMCC 1.10835	GCA_900142385.1	564117	564117	type	True	80.1419	280	460	95	below_threshold
Marinobacter aromaticivorans	strain=D15-8P	GCA_002806975.1	1494078	1494078	type	True	79.8785	290	460	95	below_threshold
Marinobacter maroccanus	strain=N4	GCA_002933275.1	2055143	2055143	type	True	77.7575	143	460	95	below_threshold
Marinobacter adhaerens	strain=HP15	GCA_000166295.1	1033846	1033846	type	True	77.7297	137	460	95	below_threshold
Marinobacter flavimaris	strain=LMG 23834	GCA_002933295.1	262076	262076	type	True	77.6939	139	460	95	below_threshold
Marinobacter flavimaris	strain=KCTC 12185	GCA_003363485.1	262076	262076	type	True	77.6703	140	460	95	below_threshold
Marinobacter sediminum	strain=R65	GCA_016820575.1	256323	256323	type	True	77.6145	117	460	95	below_threshold
Marinobacter salinexigens	strain=ZYF650	GCA_008370345.1	2919747	2919747	type	True	77.6092	100	460	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	77.586	132	460	95	below_threshold
Marinobacter gelidimuriae	strain=BF04_CF-4	GCA_000372805.1	2739064	2739064	type	True	77.0571	82	460	95	below_threshold
Marinobacter psychrophilus	strain=20041	GCA_001043175.1	330734	330734	type	True	76.833	90	460	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:09:56,366] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38962/tc_result.tsv
[2023-03-18 03:09:56,366] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:09:56,366] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:09:56,366] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg236dddcf-794f-43b8-84c6-878b44a70dd1/dqc_reference/checkm_data
[2023-03-18 03:09:56,367] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:09:56,371] [INFO] Task started: CheckM
[2023-03-18 03:09:56,371] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38962/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38962/checkm_input OceanDNA-b38962/checkm_result
[2023-03-18 03:10:25,069] [INFO] Task succeeded: CheckM
[2023-03-18 03:10:25,069] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.66%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:10:25,072] [INFO] ===== Completeness check finished =====
[2023-03-18 03:10:25,072] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:10:25,072] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38962/markers.fasta)
[2023-03-18 03:10:25,072] [INFO] Task started: Blastn
[2023-03-18 03:10:25,072] [INFO] Running command: blastn -query OceanDNA-b38962/markers.fasta -db /var/lib/cwl/stg236dddcf-794f-43b8-84c6-878b44a70dd1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38962/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:10:25,901] [INFO] Task succeeded: Blastn
[2023-03-18 03:10:25,902] [INFO] Selected 11 target genomes.
[2023-03-18 03:10:25,902] [INFO] Target genome list was writen to OceanDNA-b38962/target_genomes_gtdb.txt
[2023-03-18 03:10:25,911] [INFO] Task started: fastANI
[2023-03-18 03:10:25,912] [INFO] Running command: fastANI --query /var/lib/cwl/stg5e2517db-afc5-4343-9b91-3ff7318e90c5/OceanDNA-b38962.fa --refList OceanDNA-b38962/target_genomes_gtdb.txt --output OceanDNA-b38962/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:10:33,436] [INFO] Task succeeded: fastANI
[2023-03-18 03:10:33,443] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 03:10:33,443] [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_016597725.1	s__Marinobacter sp016597725	98.1576	443	460	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018860765.1	s__Marinobacter salexigens_A	92.0379	426	460	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016597815.1	s__Marinobacter sp016597815	81.2394	345	460	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.88	97.88	0.89	0.89	2	-
GCF_002806945.1	s__Marinobacter salexigens	80.6998	323	460	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007671675.1	s__Marinobacter maritimus	80.4758	331	460	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.91	98.91	0.93	0.93	2	-
GCF_001858325.1	s__Marinobacter sp001858325	80.1906	313	460	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	95.26	95.26	0.85	0.85	2	-
GCF_900142385.1	s__Marinobacter antarcticus	80.1419	280	460	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002806975.1	s__Marinobacter aromaticivorans	79.8785	290	460	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900215155.1	s__Marinobacter sp900215155	79.7831	291	460	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.10	97.17	0.88	0.86	3	-
GCF_002407605.1	s__Marinobacter sp002407605	79.4676	244	460	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011049865.1	s__Marinobacter antarcticus_A	79.2452	226	460	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:10:33,443] [INFO] GTDB search result was written to OceanDNA-b38962/result_gtdb.tsv
[2023-03-18 03:10:33,443] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:10:33,445] [INFO] DFAST_QC result json was written to OceanDNA-b38962/dqc_result.json
[2023-03-18 03:10:33,445] [INFO] DFAST_QC completed!
[2023-03-18 03:10:33,445] [INFO] Total running time: 0h0m58s