[2024-01-24 15:06:36,830] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:06:36,832] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:06:36,832] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f082bfb-c27d-4ff5-afd7-6df285f6b2a6/dqc_reference
[2024-01-24 15:06:38,160] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:06:38,161] [INFO] Task started: Prodigal
[2024-01-24 15:06:38,161] [INFO] Running command: gunzip -c /var/lib/cwl/stg6eab512b-24ad-4be1-a1c6-b3b3c8655129/GCF_003287735.1_ASM328773v1_genomic.fna.gz | prodigal -d GCF_003287735.1_ASM328773v1_genomic.fna/cds.fna -a GCF_003287735.1_ASM328773v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:06:50,564] [INFO] Task succeeded: Prodigal
[2024-01-24 15:06:50,564] [INFO] Task started: HMMsearch
[2024-01-24 15:06:50,564] [INFO] Running command: hmmsearch --tblout GCF_003287735.1_ASM328773v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f082bfb-c27d-4ff5-afd7-6df285f6b2a6/dqc_reference/reference_markers.hmm GCF_003287735.1_ASM328773v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:06:50,905] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:06:50,907] [INFO] Found 6/6 markers.
[2024-01-24 15:06:50,960] [INFO] Query marker FASTA was written to GCF_003287735.1_ASM328773v1_genomic.fna/markers.fasta
[2024-01-24 15:06:50,961] [INFO] Task started: Blastn
[2024-01-24 15:06:50,961] [INFO] Running command: blastn -query GCF_003287735.1_ASM328773v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f082bfb-c27d-4ff5-afd7-6df285f6b2a6/dqc_reference/reference_markers.fasta -out GCF_003287735.1_ASM328773v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:06:51,781] [INFO] Task succeeded: Blastn
[2024-01-24 15:06:51,785] [INFO] Selected 9 target genomes.
[2024-01-24 15:06:51,785] [INFO] Target genome list was writen to GCF_003287735.1_ASM328773v1_genomic.fna/target_genomes.txt
[2024-01-24 15:06:51,788] [INFO] Task started: fastANI
[2024-01-24 15:06:51,788] [INFO] Running command: fastANI --query /var/lib/cwl/stg6eab512b-24ad-4be1-a1c6-b3b3c8655129/GCF_003287735.1_ASM328773v1_genomic.fna.gz --refList GCF_003287735.1_ASM328773v1_genomic.fna/target_genomes.txt --output GCF_003287735.1_ASM328773v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:07:09,908] [INFO] Task succeeded: fastANI
[2024-01-24 15:07:09,909] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f082bfb-c27d-4ff5-afd7-6df285f6b2a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:07:09,910] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f082bfb-c27d-4ff5-afd7-6df285f6b2a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:07:09,921] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 15:07:09,922] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 15:07:09,922] [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
Photorhabdus bodei	strain=LJ24-63	GCA_003287735.1	2029681	2029681	type	True	100.0	1602	1608	95	inconclusive
Photorhabdus kleinii	strain=DSM 23513	GCA_025384885.1	768034	768034	type	True	96.4793	1381	1608	95	inconclusive
Photorhabdus kayaii	strain=DSM 15194	GCA_025384895.1	230088	230088	type	True	96.3189	1367	1608	95	inconclusive
Photorhabdus laumondii subsp. clarkei	strain=BOJ-47	GCA_003287575.1	2029685	2218628	type	True	94.8109	1368	1608	95	below_threshold
Photorhabdus laumondii subsp. laumondii	strain=TT01	GCA_003343245.1	141679	2218628	type	True	94.4525	1421	1608	95	below_threshold
Photorhabdus akhurstii	strain=DSM 15138	GCA_018448925.1	171438	171438	type	True	92.5073	1358	1608	95	below_threshold
Photorhabdus hindustanensis	strain=H1	GCA_002968995.1	2918802	2918802	type	True	92.4732	1341	1608	95	below_threshold
Photorhabdus noenieputensis	strain=DSM 25462	GCA_023108895.1	1208607	1208607	type	True	92.4386	1345	1608	95	below_threshold
Photorhabdus temperata	strain=DSM 14550	GCA_025384845.1	574560	574560	type	True	86.7546	1170	1608	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:07:09,924] [INFO] DFAST Taxonomy check result was written to GCF_003287735.1_ASM328773v1_genomic.fna/tc_result.tsv
[2024-01-24 15:07:09,924] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:07:09,924] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:07:09,924] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f082bfb-c27d-4ff5-afd7-6df285f6b2a6/dqc_reference/checkm_data
[2024-01-24 15:07:09,926] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:07:09,977] [INFO] Task started: CheckM
[2024-01-24 15:07:09,978] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003287735.1_ASM328773v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003287735.1_ASM328773v1_genomic.fna/checkm_input GCF_003287735.1_ASM328773v1_genomic.fna/checkm_result
[2024-01-24 15:07:51,946] [INFO] Task succeeded: CheckM
[2024-01-24 15:07:51,947] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:07:51,970] [INFO] ===== Completeness check finished =====
[2024-01-24 15:07:51,970] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:07:51,971] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003287735.1_ASM328773v1_genomic.fna/markers.fasta)
[2024-01-24 15:07:51,971] [INFO] Task started: Blastn
[2024-01-24 15:07:51,971] [INFO] Running command: blastn -query GCF_003287735.1_ASM328773v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f082bfb-c27d-4ff5-afd7-6df285f6b2a6/dqc_reference/reference_markers_gtdb.fasta -out GCF_003287735.1_ASM328773v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:07:53,159] [INFO] Task succeeded: Blastn
[2024-01-24 15:07:53,162] [INFO] Selected 8 target genomes.
[2024-01-24 15:07:53,162] [INFO] Target genome list was writen to GCF_003287735.1_ASM328773v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:07:53,230] [INFO] Task started: fastANI
[2024-01-24 15:07:53,231] [INFO] Running command: fastANI --query /var/lib/cwl/stg6eab512b-24ad-4be1-a1c6-b3b3c8655129/GCF_003287735.1_ASM328773v1_genomic.fna.gz --refList GCF_003287735.1_ASM328773v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003287735.1_ASM328773v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:08:08,141] [INFO] Task succeeded: fastANI
[2024-01-24 15:08:08,151] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:08:08,151] [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_003287735.1	s__Photorhabdus bodei	100.0	1602	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	97.51	96.35	0.89	0.86	10	conclusive
GCF_003343245.1	s__Photorhabdus laumondii	94.4565	1420	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	99.39	97.32	0.96	0.88	22	-
GCF_018448925.1	s__Photorhabdus akhurstii	92.4969	1358	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.2863	97.65	96.64	0.91	0.87	12	-
GCF_003545805.1	s__Photorhabdus sp003545805	92.4959	1303	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018448935.1	s__Photorhabdus noenieputensis	92.3853	1324	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001684335.1	s__Photorhabdus namnaonensis	92.2065	1345	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.2863	N/A	N/A	N/A	N/A	1	-
GCF_018448885.1	s__Photorhabdus caribbeanensis	92.1601	1331	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001083805.1	s__Photorhabdus luminescens	91.5942	1350	1608	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Photorhabdus	95.0	97.45	96.24	0.90	0.85	5	-
--------------------------------------------------------------------------------
[2024-01-24 15:08:08,153] [INFO] GTDB search result was written to GCF_003287735.1_ASM328773v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:08:08,154] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:08:08,157] [INFO] DFAST_QC result json was written to GCF_003287735.1_ASM328773v1_genomic.fna/dqc_result.json
[2024-01-24 15:08:08,157] [INFO] DFAST_QC completed!
[2024-01-24 15:08:08,157] [INFO] Total running time: 0h1m31s