[2024-01-24 12:51:06,448] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:51:06,450] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:51:06,450] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf5d0b89-37a6-413f-af06-5547ca4e5ccb/dqc_reference
[2024-01-24 12:51:07,613] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:51:07,614] [INFO] Task started: Prodigal
[2024-01-24 12:51:07,615] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd4c1f45-3abd-4dcd-b959-1eedb90d45fe/GCF_003390885.1_ASM339088v1_genomic.fna.gz | prodigal -d GCF_003390885.1_ASM339088v1_genomic.fna/cds.fna -a GCF_003390885.1_ASM339088v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:51:17,279] [INFO] Task succeeded: Prodigal
[2024-01-24 12:51:17,280] [INFO] Task started: HMMsearch
[2024-01-24 12:51:17,280] [INFO] Running command: hmmsearch --tblout GCF_003390885.1_ASM339088v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf5d0b89-37a6-413f-af06-5547ca4e5ccb/dqc_reference/reference_markers.hmm GCF_003390885.1_ASM339088v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:51:17,480] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:51:17,481] [INFO] Found 6/6 markers.
[2024-01-24 12:51:17,508] [INFO] Query marker FASTA was written to GCF_003390885.1_ASM339088v1_genomic.fna/markers.fasta
[2024-01-24 12:51:17,508] [INFO] Task started: Blastn
[2024-01-24 12:51:17,508] [INFO] Running command: blastn -query GCF_003390885.1_ASM339088v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf5d0b89-37a6-413f-af06-5547ca4e5ccb/dqc_reference/reference_markers.fasta -out GCF_003390885.1_ASM339088v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:51:18,384] [INFO] Task succeeded: Blastn
[2024-01-24 12:51:18,388] [INFO] Selected 12 target genomes.
[2024-01-24 12:51:18,388] [INFO] Target genome list was writen to GCF_003390885.1_ASM339088v1_genomic.fna/target_genomes.txt
[2024-01-24 12:51:18,400] [INFO] Task started: fastANI
[2024-01-24 12:51:18,400] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd4c1f45-3abd-4dcd-b959-1eedb90d45fe/GCF_003390885.1_ASM339088v1_genomic.fna.gz --refList GCF_003390885.1_ASM339088v1_genomic.fna/target_genomes.txt --output GCF_003390885.1_ASM339088v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:51:27,572] [INFO] Task succeeded: fastANI
[2024-01-24 12:51:27,572] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf5d0b89-37a6-413f-af06-5547ca4e5ccb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:51:27,573] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf5d0b89-37a6-413f-af06-5547ca4e5ccb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:51:27,583] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:51:27,583] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:51:27,583] [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 sediminicola	strain=IMCC34151	GCA_003390885.1	2248761	2248761	type	True	100.0	1065	1065	95	conclusive
Pelagibacterium limicola	strain=NAJP-14	GCA_015694405.1	2791022	2791022	type	True	80.7183	571	1065	95	below_threshold
Pelagibacterium lacus	strain=XYN52	GCA_003345525.1	2282655	2282655	type	True	80.1432	533	1065	95	below_threshold
Pelagibacterium halotolerans	strain=B2	GCA_000230555.1	531813	531813	type	True	79.6075	487	1065	95	below_threshold
Pelagibacterium montanilacus	strain=CCL18	GCA_003992665.1	2185280	2185280	type	True	79.3739	445	1065	95	below_threshold
Pelagibacterium xiamenense	strain=HS1C4-1	GCA_021166475.1	2901140	2901140	type	True	79.1878	430	1065	95	below_threshold
Pelagibacterium lentulum	strain=B2	GCA_003992625.1	2029865	2029865	type	True	78.3346	354	1065	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	77.7703	275	1065	95	below_threshold
Devosia marina	strain=L53-10-65	GCA_009758415.1	2683198	2683198	type	True	77.6182	257	1065	95	below_threshold
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	77.4595	326	1065	95	below_threshold
Bradyrhizobium diazoefficiens	strain=USDA 110	GCA_001642675.1	1355477	1355477	type	True	76.4493	170	1065	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	76.4122	161	1065	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:51:27,585] [INFO] DFAST Taxonomy check result was written to GCF_003390885.1_ASM339088v1_genomic.fna/tc_result.tsv
[2024-01-24 12:51:27,586] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:51:27,586] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:51:27,587] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf5d0b89-37a6-413f-af06-5547ca4e5ccb/dqc_reference/checkm_data
[2024-01-24 12:51:27,587] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:51:27,620] [INFO] Task started: CheckM
[2024-01-24 12:51:27,620] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003390885.1_ASM339088v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003390885.1_ASM339088v1_genomic.fna/checkm_input GCF_003390885.1_ASM339088v1_genomic.fna/checkm_result
[2024-01-24 12:51:58,596] [INFO] Task succeeded: CheckM
[2024-01-24 12:51:58,597] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:51:58,615] [INFO] ===== Completeness check finished =====
[2024-01-24 12:51:58,615] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:51:58,616] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003390885.1_ASM339088v1_genomic.fna/markers.fasta)
[2024-01-24 12:51:58,616] [INFO] Task started: Blastn
[2024-01-24 12:51:58,616] [INFO] Running command: blastn -query GCF_003390885.1_ASM339088v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf5d0b89-37a6-413f-af06-5547ca4e5ccb/dqc_reference/reference_markers_gtdb.fasta -out GCF_003390885.1_ASM339088v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:52:00,314] [INFO] Task succeeded: Blastn
[2024-01-24 12:52:00,317] [INFO] Selected 11 target genomes.
[2024-01-24 12:52:00,318] [INFO] Target genome list was writen to GCF_003390885.1_ASM339088v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:52:00,342] [INFO] Task started: fastANI
[2024-01-24 12:52:00,343] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd4c1f45-3abd-4dcd-b959-1eedb90d45fe/GCF_003390885.1_ASM339088v1_genomic.fna.gz --refList GCF_003390885.1_ASM339088v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003390885.1_ASM339088v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:52:08,360] [INFO] Task succeeded: fastANI
[2024-01-24 12:52:08,370] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:52:08,370] [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_003390885.1	s__Pelagibacterium sp003390885	100.0	1065	1065	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_015694405.1	s__Pelagibacterium limicola	80.7182	571	1065	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003345525.1	s__Pelagibacterium lacus	80.1663	530	1065	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000230555.1	s__Pelagibacterium halotolerans	79.5886	489	1065	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCA_002723255.1	s__Pelagibacterium sp002723255	79.5069	408	1065	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	98.69	98.23	0.81	0.73	4	-
GCA_002375765.1	s__Pelagibacterium sp002375765	79.5068	483	1065	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	79.4393	471	1065	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	99.90	99.87	0.93	0.91	4	-
GCF_003992665.1	s__Pelagibacterium montanilacus	79.3521	448	1065	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003992625.1	s__Pelagibacterium lentulum	78.3353	354	1065	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	99.98	99.98	0.99	0.99	2	-
GCF_900110945.1	s__Devosia sp900110945	77.5576	267	1065	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903828145.1	s__Devosia_A sp903828145	77.12	189	1065	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	99.95	99.93	0.97	0.97	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:52:08,372] [INFO] GTDB search result was written to GCF_003390885.1_ASM339088v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:52:08,373] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:52:08,376] [INFO] DFAST_QC result json was written to GCF_003390885.1_ASM339088v1_genomic.fna/dqc_result.json
[2024-01-24 12:52:08,377] [INFO] DFAST_QC completed!
[2024-01-24 12:52:08,377] [INFO] Total running time: 0h1m2s