[2023-06-05 12:35:02,474] [INFO] DFAST_QC pipeline started.
[2023-06-05 12:35:02,476] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 12:35:02,476] [INFO] DQC Reference Directory: /var/lib/cwl/stg11567ce2-1d1a-41ae-aa08-f9c5f517f80e/dqc_reference
[2023-06-05 12:35:03,563] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 12:35:03,564] [INFO] Task started: Prodigal
[2023-06-05 12:35:03,564] [INFO] Running command: gunzip -c /var/lib/cwl/stgf5b5cc0f-ca4b-4101-8622-9296f6436b2c/GCA_902617205.1_AG-919-N04_genomic.fna.gz | prodigal -d GCA_902617205.1_AG-919-N04_genomic.fna/cds.fna -a GCA_902617205.1_AG-919-N04_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 12:35:04,650] [INFO] Task succeeded: Prodigal
[2023-06-05 12:35:04,650] [INFO] Task started: HMMsearch
[2023-06-05 12:35:04,650] [INFO] Running command: hmmsearch --tblout GCA_902617205.1_AG-919-N04_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11567ce2-1d1a-41ae-aa08-f9c5f517f80e/dqc_reference/reference_markers.hmm GCA_902617205.1_AG-919-N04_genomic.fna/protein.faa > /dev/null
[2023-06-05 12:35:04,799] [INFO] Task succeeded: HMMsearch
[2023-06-05 12:35:04,800] [INFO] Found 6/6 markers.
[2023-06-05 12:35:04,811] [INFO] Query marker FASTA was written to GCA_902617205.1_AG-919-N04_genomic.fna/markers.fasta
[2023-06-05 12:35:04,811] [INFO] Task started: Blastn
[2023-06-05 12:35:04,811] [INFO] Running command: blastn -query GCA_902617205.1_AG-919-N04_genomic.fna/markers.fasta -db /var/lib/cwl/stg11567ce2-1d1a-41ae-aa08-f9c5f517f80e/dqc_reference/reference_markers.fasta -out GCA_902617205.1_AG-919-N04_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 12:35:05,323] [INFO] Task succeeded: Blastn
[2023-06-05 12:35:05,326] [INFO] Selected 23 target genomes.
[2023-06-05 12:35:05,326] [INFO] Target genome list was writen to GCA_902617205.1_AG-919-N04_genomic.fna/target_genomes.txt
[2023-06-05 12:35:05,332] [INFO] Task started: fastANI
[2023-06-05 12:35:05,332] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5b5cc0f-ca4b-4101-8622-9296f6436b2c/GCA_902617205.1_AG-919-N04_genomic.fna.gz --refList GCA_902617205.1_AG-919-N04_genomic.fna/target_genomes.txt --output GCA_902617205.1_AG-919-N04_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 12:35:14,896] [INFO] Task succeeded: fastANI
[2023-06-05 12:35:14,896] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11567ce2-1d1a-41ae-aa08-f9c5f517f80e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 12:35:14,897] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11567ce2-1d1a-41ae-aa08-f9c5f517f80e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 12:35:14,898] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 12:35:14,898] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 12:35:14,898] [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 12:35:14,900] [INFO] DFAST Taxonomy check result was written to GCA_902617205.1_AG-919-N04_genomic.fna/tc_result.tsv
[2023-06-05 12:35:14,900] [INFO] ===== Taxonomy check completed =====
[2023-06-05 12:35:14,900] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 12:35:14,901] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11567ce2-1d1a-41ae-aa08-f9c5f517f80e/dqc_reference/checkm_data
[2023-06-05 12:35:14,903] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 12:35:14,913] [INFO] Task started: CheckM
[2023-06-05 12:35:14,914] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902617205.1_AG-919-N04_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902617205.1_AG-919-N04_genomic.fna/checkm_input GCA_902617205.1_AG-919-N04_genomic.fna/checkm_result
[2023-06-05 12:35:25,127] [INFO] Task succeeded: CheckM
[2023-06-05 12:35:25,128] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 44.79%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 12:35:25,142] [INFO] ===== Completeness check finished =====
[2023-06-05 12:35:25,142] [INFO] ===== Start GTDB Search =====
[2023-06-05 12:35:25,142] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902617205.1_AG-919-N04_genomic.fna/markers.fasta)
[2023-06-05 12:35:25,142] [INFO] Task started: Blastn
[2023-06-05 12:35:25,143] [INFO] Running command: blastn -query GCA_902617205.1_AG-919-N04_genomic.fna/markers.fasta -db /var/lib/cwl/stg11567ce2-1d1a-41ae-aa08-f9c5f517f80e/dqc_reference/reference_markers_gtdb.fasta -out GCA_902617205.1_AG-919-N04_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 12:35:25,865] [INFO] Task succeeded: Blastn
[2023-06-05 12:35:25,868] [INFO] Selected 6 target genomes.
[2023-06-05 12:35:25,868] [INFO] Target genome list was writen to GCA_902617205.1_AG-919-N04_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 12:35:25,872] [INFO] Task started: fastANI
[2023-06-05 12:35:25,872] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5b5cc0f-ca4b-4101-8622-9296f6436b2c/GCA_902617205.1_AG-919-N04_genomic.fna.gz --refList GCA_902617205.1_AG-919-N04_genomic.fna/target_genomes_gtdb.txt --output GCA_902617205.1_AG-919-N04_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 12:35:26,992] [INFO] Task succeeded: fastANI
[2023-06-05 12:35:26,997] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 12:35:26,997] [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_000402655.1	s__Marinisoma sp000402655	95.8697	214	230	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	96.42	95.83	0.93	0.92	4	conclusive
GCA_902538565.1	s__Marinisoma sp902538565	88.3553	211	230	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	99.07	99.04	0.96	0.96	3	-
GCA_902576865.1	s__Marinisoma sp902576865	88.1416	168	230	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	96.64	96.64	0.80	0.80	2	-
GCA_902525615.1	s__Marinisoma sp902525615	87.5019	191	230	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902599655.1	s__Marinisoma sp902599655	87.0721	147	230	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	97.53	97.28	0.66	0.66	3	-
GCA_902624275.1	s__Marinisoma sp902624275	85.6449	177	230	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 12:35:26,999] [INFO] GTDB search result was written to GCA_902617205.1_AG-919-N04_genomic.fna/result_gtdb.tsv
[2023-06-05 12:35:27,000] [INFO] ===== GTDB Search completed =====
[2023-06-05 12:35:27,002] [INFO] DFAST_QC result json was written to GCA_902617205.1_AG-919-N04_genomic.fna/dqc_result.json
[2023-06-05 12:35:27,002] [INFO] DFAST_QC completed!
[2023-06-05 12:35:27,002] [INFO] Total running time: 0h0m25s