[2023-03-15 03:14:16,438] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:14:16,438] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:14:16,439] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a4b8d6e-1621-4abb-82a1-605fbde40b1c/dqc_reference
[2023-03-15 03:14:17,607] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:14:17,608] [INFO] Task started: Prodigal
[2023-03-15 03:14:17,608] [INFO] Running command: cat /var/lib/cwl/stg3bd17cdb-fa5b-419f-b3f1-4af402a9f67e/OceanDNA-b26701.fa | prodigal -d OceanDNA-b26701/cds.fna -a OceanDNA-b26701/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:14:28,205] [INFO] Task succeeded: Prodigal
[2023-03-15 03:14:28,206] [INFO] Task started: HMMsearch
[2023-03-15 03:14:28,206] [INFO] Running command: hmmsearch --tblout OceanDNA-b26701/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a4b8d6e-1621-4abb-82a1-605fbde40b1c/dqc_reference/reference_markers.hmm OceanDNA-b26701/protein.faa > /dev/null
[2023-03-15 03:14:28,349] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:14:28,350] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg3bd17cdb-fa5b-419f-b3f1-4af402a9f67e/OceanDNA-b26701.fa]
[2023-03-15 03:14:28,365] [INFO] Query marker FASTA was written to OceanDNA-b26701/markers.fasta
[2023-03-15 03:14:28,366] [INFO] Task started: Blastn
[2023-03-15 03:14:28,366] [INFO] Running command: blastn -query OceanDNA-b26701/markers.fasta -db /var/lib/cwl/stg4a4b8d6e-1621-4abb-82a1-605fbde40b1c/dqc_reference/reference_markers.fasta -out OceanDNA-b26701/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:14:28,838] [INFO] Task succeeded: Blastn
[2023-03-15 03:14:28,839] [INFO] Selected 11 target genomes.
[2023-03-15 03:14:28,839] [INFO] Target genome list was writen to OceanDNA-b26701/target_genomes.txt
[2023-03-15 03:14:28,846] [INFO] Task started: fastANI
[2023-03-15 03:14:28,847] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bd17cdb-fa5b-419f-b3f1-4af402a9f67e/OceanDNA-b26701.fa --refList OceanDNA-b26701/target_genomes.txt --output OceanDNA-b26701/fastani_result.tsv --threads 1
[2023-03-15 03:14:35,962] [INFO] Task succeeded: fastANI
[2023-03-15 03:14:35,963] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a4b8d6e-1621-4abb-82a1-605fbde40b1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:14:35,963] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a4b8d6e-1621-4abb-82a1-605fbde40b1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:14:35,970] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:14:35,970] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 03:14:35,970] [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
Pelagibacterium halotolerans	strain=B2	GCA_000230555.1	531813	531813	type	True	86.703	426	541	95	below_threshold
Pelagibacterium lacus	strain=XYN52	GCA_003345525.1	2282655	2282655	type	True	80.0563	251	541	95	below_threshold
Pelagibacterium luteolum	strain=CGMCC 1.10267	GCA_900100665.1	440168	440168	type	True	79.3954	266	541	95	below_threshold
Pelagibacterium sediminicola	strain=IMCC34151	GCA_003390885.1	2248761	2248761	type	True	79.0135	222	541	95	below_threshold
Pelagibacterium xiamenense	strain=HS1C4-1	GCA_021166475.1	2901140	2901140	type	True	77.8694	196	541	95	below_threshold
Pelagibacterium lentulum	strain=B2	GCA_003992625.1	2029865	2029865	type	True	77.8116	143	541	95	below_threshold
Arsenicitalea aurantiaca	strain=42-50	GCA_003994485.1	1783274	1783274	type	True	77.7148	117	541	95	below_threshold
Devosia elaeis	strain=S37	GCA_001650025.1	1770058	1770058	type	True	76.9918	135	541	95	below_threshold
Devosia sediminis	strain=MSA67	GCA_016411825.1	2798801	2798801	type	True	76.977	128	541	95	below_threshold
Devosia submarina	strain=JCM 18935	GCA_003056345.1	1173082	1173082	type	True	76.8392	80	541	95	below_threshold
Devosia soli	strain=GH2-10	GCA_000970455.1	361041	361041	type	True	76.7746	97	541	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 03:14:35,971] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26701/tc_result.tsv
[2023-03-15 03:14:35,971] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:14:35,971] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:14:35,971] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a4b8d6e-1621-4abb-82a1-605fbde40b1c/dqc_reference/checkm_data
[2023-03-15 03:14:35,972] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:14:35,976] [INFO] Task started: CheckM
[2023-03-15 03:14:35,976] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26701/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26701/checkm_input OceanDNA-b26701/checkm_result
[2023-03-15 03:15:06,500] [INFO] Task succeeded: CheckM
[2023-03-15 03:15:06,501] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 29.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:15:06,503] [INFO] ===== Completeness check finished =====
[2023-03-15 03:15:06,503] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:15:06,503] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26701/markers.fasta)
[2023-03-15 03:15:06,503] [INFO] Task started: Blastn
[2023-03-15 03:15:06,503] [INFO] Running command: blastn -query OceanDNA-b26701/markers.fasta -db /var/lib/cwl/stg4a4b8d6e-1621-4abb-82a1-605fbde40b1c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26701/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:15:07,056] [INFO] Task succeeded: Blastn
[2023-03-15 03:15:07,056] [INFO] Selected 8 target genomes.
[2023-03-15 03:15:07,056] [INFO] Target genome list was writen to OceanDNA-b26701/target_genomes_gtdb.txt
[2023-03-15 03:15:07,066] [INFO] Task started: fastANI
[2023-03-15 03:15:07,066] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bd17cdb-fa5b-419f-b3f1-4af402a9f67e/OceanDNA-b26701.fa --refList OceanDNA-b26701/target_genomes_gtdb.txt --output OceanDNA-b26701/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:15:12,202] [INFO] Task succeeded: fastANI
[2023-03-15 03:15:12,207] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 03:15:12,208] [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_002723255.1	s__Pelagibacterium sp002723255	91.8152	382	541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	98.69	98.23	0.81	0.73	4	-
GCF_000230555.1	s__Pelagibacterium halotolerans	86.703	426	541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCA_002375765.1	s__Pelagibacterium sp002375765	86.1925	412	541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	99.84	99.84	0.95	0.95	2	-
GCA_002337455.1	s__Pelagibacterium sp002337455	85.4464	406	541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	99.90	99.87	0.93	0.91	4	-
GCF_003345525.1	s__Pelagibacterium lacus	80.0781	250	541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100665.1	s__Pelagibacterium luteolum	79.3766	267	541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390885.1	s__Pelagibacterium sp003390885	79.0135	222	541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017307495.1	s__Devosia_A sp017307495	77.0572	103	541	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	98.70	98.70	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2023-03-15 03:15:12,208] [INFO] GTDB search result was written to OceanDNA-b26701/result_gtdb.tsv
[2023-03-15 03:15:12,208] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:15:12,209] [INFO] DFAST_QC result json was written to OceanDNA-b26701/dqc_result.json
[2023-03-15 03:15:12,209] [INFO] DFAST_QC completed!
[2023-03-15 03:15:12,209] [INFO] Total running time: 0h0m56s