[2023-03-15 06:28:21,336] [INFO] DFAST_QC pipeline started.
[2023-03-15 06:28:21,336] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 06:28:21,337] [INFO] DQC Reference Directory: /var/lib/cwl/stgd5fba21a-8d49-4114-b935-1c232af3974b/dqc_reference
[2023-03-15 06:28:22,448] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 06:28:22,449] [INFO] Task started: Prodigal
[2023-03-15 06:28:22,449] [INFO] Running command: cat /var/lib/cwl/stgd2c289b8-fb45-4c60-bb0b-aba2beda6d7b/OceanDNA-b38493.fa | prodigal -d OceanDNA-b38493/cds.fna -a OceanDNA-b38493/protein.faa -g 11 -q > /dev/null
[2023-03-15 06:28:30,380] [INFO] Task succeeded: Prodigal
[2023-03-15 06:28:30,381] [INFO] Task started: HMMsearch
[2023-03-15 06:28:30,381] [INFO] Running command: hmmsearch --tblout OceanDNA-b38493/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd5fba21a-8d49-4114-b935-1c232af3974b/dqc_reference/reference_markers.hmm OceanDNA-b38493/protein.faa > /dev/null
[2023-03-15 06:28:30,508] [INFO] Task succeeded: HMMsearch
[2023-03-15 06:28:30,508] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgd2c289b8-fb45-4c60-bb0b-aba2beda6d7b/OceanDNA-b38493.fa]
[2023-03-15 06:28:30,552] [INFO] Query marker FASTA was written to OceanDNA-b38493/markers.fasta
[2023-03-15 06:28:30,553] [INFO] Task started: Blastn
[2023-03-15 06:28:30,553] [INFO] Running command: blastn -query OceanDNA-b38493/markers.fasta -db /var/lib/cwl/stgd5fba21a-8d49-4114-b935-1c232af3974b/dqc_reference/reference_markers.fasta -out OceanDNA-b38493/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:28:31,028] [INFO] Task succeeded: Blastn
[2023-03-15 06:28:31,028] [INFO] Selected 7 target genomes.
[2023-03-15 06:28:31,029] [INFO] Target genome list was writen to OceanDNA-b38493/target_genomes.txt
[2023-03-15 06:28:31,032] [INFO] Task started: fastANI
[2023-03-15 06:28:31,033] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2c289b8-fb45-4c60-bb0b-aba2beda6d7b/OceanDNA-b38493.fa --refList OceanDNA-b38493/target_genomes.txt --output OceanDNA-b38493/fastani_result.tsv --threads 1
[2023-03-15 06:28:35,938] [INFO] Task succeeded: fastANI
[2023-03-15 06:28:35,938] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd5fba21a-8d49-4114-b935-1c232af3974b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 06:28:35,938] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd5fba21a-8d49-4114-b935-1c232af3974b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 06:28:35,944] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 06:28:35,944] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 06:28:35,944] [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
Marinomonas foliarum	strain=CECT 7731	GCA_003337275.1	491950	491950	type	True	88.3203	433	475	95	below_threshold
Marinomonas alcarazii	strain=CECT 7730	GCA_003208215.1	491949	491949	type	True	87.0906	414	475	95	below_threshold
Marinomonas lutimaris	strain=E165	GCA_019426345.1	2846746	2846746	type	True	82.5174	355	475	95	below_threshold
Marinomonas polaris	strain=DSM 16579	GCA_900129155.1	293552	293552	type	True	81.8487	354	475	95	below_threshold
Marinomonas rhizomae	strain=IVIA-Po-145	GCA_003721275.1	491948	491948	type	True	81.2973	327	475	95	below_threshold
Marinomonas rhizomae	strain=CECT 7377	GCA_003315485.1	491948	491948	type	True	81.2783	324	475	95	below_threshold
Marinomonas shanghaiensis	strain=DSL-35	GCA_003259175.1	2202418	2202418	type	True	80.2062	287	475	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 06:28:35,954] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38493/tc_result.tsv
[2023-03-15 06:28:35,954] [INFO] ===== Taxonomy check completed =====
[2023-03-15 06:28:35,955] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 06:28:35,955] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd5fba21a-8d49-4114-b935-1c232af3974b/dqc_reference/checkm_data
[2023-03-15 06:28:35,955] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 06:28:35,960] [INFO] Task started: CheckM
[2023-03-15 06:28:35,960] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38493/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38493/checkm_input OceanDNA-b38493/checkm_result
[2023-03-15 06:29:00,570] [INFO] Task succeeded: CheckM
[2023-03-15 06:29:00,570] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 06:29:00,607] [INFO] ===== Completeness check finished =====
[2023-03-15 06:29:00,607] [INFO] ===== Start GTDB Search =====
[2023-03-15 06:29:00,607] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38493/markers.fasta)
[2023-03-15 06:29:00,608] [INFO] Task started: Blastn
[2023-03-15 06:29:00,608] [INFO] Running command: blastn -query OceanDNA-b38493/markers.fasta -db /var/lib/cwl/stgd5fba21a-8d49-4114-b935-1c232af3974b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38493/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:29:01,155] [INFO] Task succeeded: Blastn
[2023-03-15 06:29:01,166] [INFO] Selected 7 target genomes.
[2023-03-15 06:29:01,166] [INFO] Target genome list was writen to OceanDNA-b38493/target_genomes_gtdb.txt
[2023-03-15 06:29:01,173] [INFO] Task started: fastANI
[2023-03-15 06:29:01,173] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2c289b8-fb45-4c60-bb0b-aba2beda6d7b/OceanDNA-b38493.fa --refList OceanDNA-b38493/target_genomes_gtdb.txt --output OceanDNA-b38493/fastani_result_gtdb.tsv --threads 1
[2023-03-15 06:29:06,223] [INFO] Task succeeded: fastANI
[2023-03-15 06:29:06,228] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 06:29:06,229] [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_003337275.1	s__Marinomonas foliarum	88.3203	433	475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.18	98.18	0.87	0.87	2	-
GCF_003208215.1	s__Marinomonas alcarazii	87.0906	414	475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.70	98.70	0.93	0.93	2	-
GCF_018336955.1	s__Marinomonas sp018336955	82.3515	359	475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000017285.1	s__Marinomonas sp000017285	82.0694	357	475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	98.39	98.39	0.88	0.88	2	-
GCF_900129155.1	s__Marinomonas polaris	81.8487	354	475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	97.53	97.35	0.90	0.88	9	-
GCF_003315485.1	s__Marinomonas rhizomae	81.2783	324	475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003259175.1	s__Marinomonas shanghaiensis	80.2062	287	475	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Marinomonadaceae;g__Marinomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 06:29:06,229] [INFO] GTDB search result was written to OceanDNA-b38493/result_gtdb.tsv
[2023-03-15 06:29:06,229] [INFO] ===== GTDB Search completed =====
[2023-03-15 06:29:06,230] [INFO] DFAST_QC result json was written to OceanDNA-b38493/dqc_result.json
[2023-03-15 06:29:06,230] [INFO] DFAST_QC completed!
[2023-03-15 06:29:06,230] [INFO] Total running time: 0h0m45s