[2023-03-18 07:29:30,335] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:29:30,335] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:29:30,336] [INFO] DQC Reference Directory: /var/lib/cwl/stg5fc9093d-aadb-46a9-aa70-e6e043ca6a49/dqc_reference
[2023-03-18 07:29:31,935] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:29:31,935] [INFO] Task started: Prodigal
[2023-03-18 07:29:31,935] [INFO] Running command: cat /var/lib/cwl/stgcd6477ce-578c-455d-8fb8-598e9d64cd0d/OceanDNA-b38947.fa | prodigal -d OceanDNA-b38947/cds.fna -a OceanDNA-b38947/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:29:57,641] [INFO] Task succeeded: Prodigal
[2023-03-18 07:29:57,641] [INFO] Task started: HMMsearch
[2023-03-18 07:29:57,641] [INFO] Running command: hmmsearch --tblout OceanDNA-b38947/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5fc9093d-aadb-46a9-aa70-e6e043ca6a49/dqc_reference/reference_markers.hmm OceanDNA-b38947/protein.faa > /dev/null
[2023-03-18 07:29:57,875] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:29:57,876] [INFO] Found 6/6 markers.
[2023-03-18 07:29:57,900] [INFO] Query marker FASTA was written to OceanDNA-b38947/markers.fasta
[2023-03-18 07:29:57,900] [INFO] Task started: Blastn
[2023-03-18 07:29:57,900] [INFO] Running command: blastn -query OceanDNA-b38947/markers.fasta -db /var/lib/cwl/stg5fc9093d-aadb-46a9-aa70-e6e043ca6a49/dqc_reference/reference_markers.fasta -out OceanDNA-b38947/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:29:58,622] [INFO] Task succeeded: Blastn
[2023-03-18 07:29:58,623] [INFO] Selected 16 target genomes.
[2023-03-18 07:29:58,623] [INFO] Target genome list was writen to OceanDNA-b38947/target_genomes.txt
[2023-03-18 07:29:58,632] [INFO] Task started: fastANI
[2023-03-18 07:29:58,632] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd6477ce-578c-455d-8fb8-598e9d64cd0d/OceanDNA-b38947.fa --refList OceanDNA-b38947/target_genomes.txt --output OceanDNA-b38947/fastani_result.tsv --threads 1
[2023-03-18 07:30:12,023] [INFO] Task succeeded: fastANI
[2023-03-18 07:30:12,023] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5fc9093d-aadb-46a9-aa70-e6e043ca6a49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:30:12,023] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5fc9093d-aadb-46a9-aa70-e6e043ca6a49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:30:12,033] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:30:12,033] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 07:30:12,033] [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 maritimus	strain=CK47	GCA_007671675.1	277961	277961	type	True	90.4143	1102	1378	95	below_threshold
Marinobacter antarcticus	strain=CGMCC 1.10835	GCA_900142385.1	564117	564117	type	True	84.872	920	1378	95	below_threshold
Marinobacter aromaticivorans	strain=D15-8P	GCA_002806975.1	1494078	1494078	type	True	81.8136	840	1378	95	below_threshold
Marinobacter salexigens	strain=HJR7	GCA_002806945.1	1925763	1925763	type	True	81.3056	772	1378	95	below_threshold
Marinobacter gelidimuriae	strain=BF04_CF-4	GCA_000372805.1	2739064	2739064	type	True	79.328	323	1378	95	below_threshold
Marinobacter piscensis	strain=Abdou3	GCA_007671655.1	1562308	1562308	type	True	79.2759	531	1378	95	below_threshold
Marinobacter flavimaris	strain=LMG 23834	GCA_002933295.1	262076	262076	type	True	78.8836	474	1378	95	below_threshold
Marinobacter guineae	strain=M3B	GCA_002744735.1	432303	432303	type	True	78.8554	517	1378	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	78.653	451	1378	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	78.5912	458	1378	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	78.5673	380	1378	95	below_threshold
Marinobacter shengliensis	strain=SL013A34A2	GCA_003007715.1	1389223	1389223	type	True	78.5633	418	1378	95	below_threshold
Marinobacter shengliensis subsp. alexandrii	strain=LZ-6	GCA_005871095.1	2570350	1389223	type	True	78.5516	417	1378	95	below_threshold
Marinobacter halophilus	strain=JCM 30472	GCA_003007685.1	1323740	1323740	type	True	78.4522	392	1378	95	below_threshold
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	78.2278	401	1378	95	below_threshold
Marinobacter bryozoorum	strain=DSM 15401	GCA_023156245.1	256324	256324	type	True	77.3257	251	1378	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 07:30:12,033] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38947/tc_result.tsv
[2023-03-18 07:30:12,033] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:30:12,033] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:30:12,034] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5fc9093d-aadb-46a9-aa70-e6e043ca6a49/dqc_reference/checkm_data
[2023-03-18 07:30:12,034] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:30:12,040] [INFO] Task started: CheckM
[2023-03-18 07:30:12,040] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38947/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38947/checkm_input OceanDNA-b38947/checkm_result
[2023-03-18 07:31:14,954] [INFO] Task succeeded: CheckM
[2023-03-18 07:31:14,954] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:31:14,957] [INFO] ===== Completeness check finished =====
[2023-03-18 07:31:14,957] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:31:14,958] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38947/markers.fasta)
[2023-03-18 07:31:14,958] [INFO] Task started: Blastn
[2023-03-18 07:31:14,958] [INFO] Running command: blastn -query OceanDNA-b38947/markers.fasta -db /var/lib/cwl/stg5fc9093d-aadb-46a9-aa70-e6e043ca6a49/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38947/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:31:16,178] [INFO] Task succeeded: Blastn
[2023-03-18 07:31:16,179] [INFO] Selected 12 target genomes.
[2023-03-18 07:31:16,179] [INFO] Target genome list was writen to OceanDNA-b38947/target_genomes_gtdb.txt
[2023-03-18 07:31:16,252] [INFO] Task started: fastANI
[2023-03-18 07:31:16,252] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd6477ce-578c-455d-8fb8-598e9d64cd0d/OceanDNA-b38947.fa --refList OceanDNA-b38947/target_genomes_gtdb.txt --output OceanDNA-b38947/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:31:27,299] [INFO] Task succeeded: fastANI
[2023-03-18 07:31:27,307] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 07:31:27,307] [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_018066865.1	s__Marinobacter sp018066865	98.7302	1012	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.94	99.94	0.89	0.89	2	conclusive
GCF_007671675.1	s__Marinobacter maritimus	90.4143	1102	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.91	98.91	0.93	0.93	2	-
GCF_900142385.1	s__Marinobacter antarcticus	84.872	920	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001858325.1	s__Marinobacter sp001858325	83.1789	908	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	95.26	95.26	0.85	0.85	2	-
GCA_011049865.1	s__Marinobacter antarcticus_A	82.4948	804	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215155.1	s__Marinobacter sp900215155	82.209	868	1378	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	82.1672	824	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003318275.1	s__Marinobacter sp003318275	81.6271	687	1378	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	81.5585	761	1378	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	81.3109	771	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016597725.1	s__Marinobacter sp016597725	81.1414	751	1378	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860765.1	s__Marinobacter salexigens_A	80.858	728	1378	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 07:31:27,408] [INFO] GTDB search result was written to OceanDNA-b38947/result_gtdb.tsv
[2023-03-18 07:31:27,409] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:31:27,430] [INFO] DFAST_QC result json was written to OceanDNA-b38947/dqc_result.json
[2023-03-18 07:31:27,430] [INFO] DFAST_QC completed!
[2023-03-18 07:31:27,430] [INFO] Total running time: 0h1m57s