[2023-06-05 18:00:52,907] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:00:52,926] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:00:52,926] [INFO] DQC Reference Directory: /var/lib/cwl/stg879bd56f-0775-4fc9-bec3-334c2007f556/dqc_reference
[2023-06-05 18:00:54,224] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:00:54,225] [INFO] Task started: Prodigal
[2023-06-05 18:00:54,226] [INFO] Running command: gunzip -c /var/lib/cwl/stged4eb1e5-e2d8-4393-895f-08be9f59e946/GCA_902627945.1_AH-321-N06_genomic.fna.gz | prodigal -d GCA_902627945.1_AH-321-N06_genomic.fna/cds.fna -a GCA_902627945.1_AH-321-N06_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:00:55,288] [INFO] Task succeeded: Prodigal
[2023-06-05 18:00:55,288] [INFO] Task started: HMMsearch
[2023-06-05 18:00:55,288] [INFO] Running command: hmmsearch --tblout GCA_902627945.1_AH-321-N06_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg879bd56f-0775-4fc9-bec3-334c2007f556/dqc_reference/reference_markers.hmm GCA_902627945.1_AH-321-N06_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:00:55,396] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:00:55,397] [WARNING] Found 3/6 markers. [/var/lib/cwl/stged4eb1e5-e2d8-4393-895f-08be9f59e946/GCA_902627945.1_AH-321-N06_genomic.fna.gz]
[2023-06-05 18:00:55,407] [INFO] Query marker FASTA was written to GCA_902627945.1_AH-321-N06_genomic.fna/markers.fasta
[2023-06-05 18:00:55,407] [INFO] Task started: Blastn
[2023-06-05 18:00:55,407] [INFO] Running command: blastn -query GCA_902627945.1_AH-321-N06_genomic.fna/markers.fasta -db /var/lib/cwl/stg879bd56f-0775-4fc9-bec3-334c2007f556/dqc_reference/reference_markers.fasta -out GCA_902627945.1_AH-321-N06_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:00:56,044] [INFO] Task succeeded: Blastn
[2023-06-05 18:00:56,060] [INFO] Selected 6 target genomes.
[2023-06-05 18:00:56,061] [INFO] Target genome list was writen to GCA_902627945.1_AH-321-N06_genomic.fna/target_genomes.txt
[2023-06-05 18:00:56,063] [INFO] Task started: fastANI
[2023-06-05 18:00:56,063] [INFO] Running command: fastANI --query /var/lib/cwl/stged4eb1e5-e2d8-4393-895f-08be9f59e946/GCA_902627945.1_AH-321-N06_genomic.fna.gz --refList GCA_902627945.1_AH-321-N06_genomic.fna/target_genomes.txt --output GCA_902627945.1_AH-321-N06_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:00:58,096] [INFO] Task succeeded: fastANI
[2023-06-05 18:00:58,096] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg879bd56f-0775-4fc9-bec3-334c2007f556/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:00:58,097] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg879bd56f-0775-4fc9-bec3-334c2007f556/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:00:58,122] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:00:58,122] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 18:00:58,123] [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
--------------------------------------------------------------------------------
[2023-06-05 18:00:58,125] [INFO] DFAST Taxonomy check result was written to GCA_902627945.1_AH-321-N06_genomic.fna/tc_result.tsv
[2023-06-05 18:00:58,126] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:00:58,126] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:00:58,127] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg879bd56f-0775-4fc9-bec3-334c2007f556/dqc_reference/checkm_data
[2023-06-05 18:00:58,129] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:00:58,137] [INFO] Task started: CheckM
[2023-06-05 18:00:58,138] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902627945.1_AH-321-N06_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902627945.1_AH-321-N06_genomic.fna/checkm_input GCA_902627945.1_AH-321-N06_genomic.fna/checkm_result
[2023-06-05 18:01:10,228] [INFO] Task succeeded: CheckM
[2023-06-05 18:01:10,229] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 12.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:01:10,264] [INFO] ===== Completeness check finished =====
[2023-06-05 18:01:10,265] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:01:10,265] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902627945.1_AH-321-N06_genomic.fna/markers.fasta)
[2023-06-05 18:01:10,265] [INFO] Task started: Blastn
[2023-06-05 18:01:10,266] [INFO] Running command: blastn -query GCA_902627945.1_AH-321-N06_genomic.fna/markers.fasta -db /var/lib/cwl/stg879bd56f-0775-4fc9-bec3-334c2007f556/dqc_reference/reference_markers_gtdb.fasta -out GCA_902627945.1_AH-321-N06_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:01:10,965] [INFO] Task succeeded: Blastn
[2023-06-05 18:01:10,969] [INFO] Selected 14 target genomes.
[2023-06-05 18:01:10,969] [INFO] Target genome list was writen to GCA_902627945.1_AH-321-N06_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:01:10,981] [INFO] Task started: fastANI
[2023-06-05 18:01:10,982] [INFO] Running command: fastANI --query /var/lib/cwl/stged4eb1e5-e2d8-4393-895f-08be9f59e946/GCA_902627945.1_AH-321-N06_genomic.fna.gz --refList GCA_902627945.1_AH-321-N06_genomic.fna/target_genomes_gtdb.txt --output GCA_902627945.1_AH-321-N06_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:01:13,522] [INFO] Task succeeded: fastANI
[2023-06-05 18:01:13,534] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 18:01:13,534] [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_902629285.1	s__Pelagibacter sp902629285	91.9796	81	98	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902624585.1	s__Pelagibacter sp902624585	88.4739	60	98	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902628275.1	s__Pelagibacter sp902628275	87.6942	69	98	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902553675.1	s__Pelagibacter sp902553675	85.5345	57	98	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902593445.1	s__Pelagibacter sp902593445	85.5085	68	98	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902578325.1	s__Pelagibacter sp902578325	85.0643	52	98	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902597555.1	s__Pelagibacter sp902597555	85.0144	65	98	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902572515.1	s__Pelagibacter sp902572515	84.9826	64	98	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902611405.1	s__Pelagibacter sp902611405	84.8329	70	98	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902599335.1	s__Pelagibacter sp902599335	84.7172	79	98	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003278805.1	s__Pelagibacter sp003278805	84.4997	76	98	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003279775.1	s__Pelagibacter sp003279775	84.4363	58	98	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	100.00	100.00	0.98	0.98	2	-
GCA_902593235.1	s__Pelagibacter sp902593235	84.3308	61	98	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__Pelagibacteraceae;g__Pelagibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 18:01:13,552] [INFO] GTDB search result was written to GCA_902627945.1_AH-321-N06_genomic.fna/result_gtdb.tsv
[2023-06-05 18:01:13,553] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:01:13,565] [INFO] DFAST_QC result json was written to GCA_902627945.1_AH-321-N06_genomic.fna/dqc_result.json
[2023-06-05 18:01:13,566] [INFO] DFAST_QC completed!
[2023-06-05 18:01:13,566] [INFO] Total running time: 0h0m21s