[2023-06-28 17:03:01,985] [INFO] DFAST_QC pipeline started.
[2023-06-28 17:03:01,987] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 17:03:01,987] [INFO] DQC Reference Directory: /var/lib/cwl/stg9de5ac05-fb10-4db1-94ff-7ce05a752ca2/dqc_reference
[2023-06-28 17:03:03,212] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 17:03:03,213] [INFO] Task started: Prodigal
[2023-06-28 17:03:03,213] [INFO] Running command: gunzip -c /var/lib/cwl/stgc811def7-a90c-418f-946a-b397a5983a40/GCA_017448655.1_ASM1744865v1_genomic.fna.gz | prodigal -d GCA_017448655.1_ASM1744865v1_genomic.fna/cds.fna -a GCA_017448655.1_ASM1744865v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 17:03:16,316] [INFO] Task succeeded: Prodigal
[2023-06-28 17:03:16,317] [INFO] Task started: HMMsearch
[2023-06-28 17:03:16,317] [INFO] Running command: hmmsearch --tblout GCA_017448655.1_ASM1744865v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9de5ac05-fb10-4db1-94ff-7ce05a752ca2/dqc_reference/reference_markers.hmm GCA_017448655.1_ASM1744865v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 17:03:16,570] [INFO] Task succeeded: HMMsearch
[2023-06-28 17:03:16,572] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc811def7-a90c-418f-946a-b397a5983a40/GCA_017448655.1_ASM1744865v1_genomic.fna.gz]
[2023-06-28 17:03:16,610] [INFO] Query marker FASTA was written to GCA_017448655.1_ASM1744865v1_genomic.fna/markers.fasta
[2023-06-28 17:03:16,610] [INFO] Task started: Blastn
[2023-06-28 17:03:16,610] [INFO] Running command: blastn -query GCA_017448655.1_ASM1744865v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9de5ac05-fb10-4db1-94ff-7ce05a752ca2/dqc_reference/reference_markers.fasta -out GCA_017448655.1_ASM1744865v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:03:17,303] [INFO] Task succeeded: Blastn
[2023-06-28 17:03:17,308] [INFO] Selected 23 target genomes.
[2023-06-28 17:03:17,308] [INFO] Target genome list was writen to GCA_017448655.1_ASM1744865v1_genomic.fna/target_genomes.txt
[2023-06-28 17:03:17,309] [INFO] Task started: fastANI
[2023-06-28 17:03:17,310] [INFO] Running command: fastANI --query /var/lib/cwl/stgc811def7-a90c-418f-946a-b397a5983a40/GCA_017448655.1_ASM1744865v1_genomic.fna.gz --refList GCA_017448655.1_ASM1744865v1_genomic.fna/target_genomes.txt --output GCA_017448655.1_ASM1744865v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 17:03:30,284] [INFO] Task succeeded: fastANI
[2023-06-28 17:03:30,285] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9de5ac05-fb10-4db1-94ff-7ce05a752ca2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 17:03:30,286] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9de5ac05-fb10-4db1-94ff-7ce05a752ca2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 17:03:30,288] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 17:03:30,288] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 17:03:30,288] [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
--------------------------------------------------------------------------------
[2023-06-28 17:03:30,291] [INFO] DFAST Taxonomy check result was written to GCA_017448655.1_ASM1744865v1_genomic.fna/tc_result.tsv
[2023-06-28 17:03:30,292] [INFO] ===== Taxonomy check completed =====
[2023-06-28 17:03:30,292] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 17:03:30,292] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9de5ac05-fb10-4db1-94ff-7ce05a752ca2/dqc_reference/checkm_data
[2023-06-28 17:03:30,297] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 17:03:30,327] [INFO] Task started: CheckM
[2023-06-28 17:03:30,328] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017448655.1_ASM1744865v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017448655.1_ASM1744865v1_genomic.fna/checkm_input GCA_017448655.1_ASM1744865v1_genomic.fna/checkm_result
[2023-06-28 17:04:09,499] [INFO] Task succeeded: CheckM
[2023-06-28 17:04:09,500] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 17:04:09,522] [INFO] ===== Completeness check finished =====
[2023-06-28 17:04:09,523] [INFO] ===== Start GTDB Search =====
[2023-06-28 17:04:09,523] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017448655.1_ASM1744865v1_genomic.fna/markers.fasta)
[2023-06-28 17:04:09,523] [INFO] Task started: Blastn
[2023-06-28 17:04:09,524] [INFO] Running command: blastn -query GCA_017448655.1_ASM1744865v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9de5ac05-fb10-4db1-94ff-7ce05a752ca2/dqc_reference/reference_markers_gtdb.fasta -out GCA_017448655.1_ASM1744865v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:04:10,648] [INFO] Task succeeded: Blastn
[2023-06-28 17:04:10,652] [INFO] Selected 12 target genomes.
[2023-06-28 17:04:10,653] [INFO] Target genome list was writen to GCA_017448655.1_ASM1744865v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 17:04:10,654] [INFO] Task started: fastANI
[2023-06-28 17:04:10,654] [INFO] Running command: fastANI --query /var/lib/cwl/stgc811def7-a90c-418f-946a-b397a5983a40/GCA_017448655.1_ASM1744865v1_genomic.fna.gz --refList GCA_017448655.1_ASM1744865v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017448655.1_ASM1744865v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 17:04:15,651] [INFO] Task succeeded: fastANI
[2023-06-28 17:04:15,663] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 17:04:15,664] [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_900318565.1	s__Cryptobacteroides sp900318565	96.861	405	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.62	96.86	0.83	0.73	9	conclusive
GCA_902782225.1	s__Cryptobacteroides sp902782225	81.5	285	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.55	97.13	0.87	0.83	3	-
GCA_017617715.1	s__Cryptobacteroides sp017617715	80.7766	249	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902780175.1	s__Cryptobacteroides sp902780175	79.9194	181	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	95.78	95.78	0.73	0.73	2	-
GCA_016288775.1	s__Cryptobacteroides sp016288775	79.8997	200	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002309995.1	s__Cryptobacteroides sp002309995	79.8977	177	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017651465.1	s__Cryptobacteroides sp017651465	79.67	212	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017561765.1	s__Cryptobacteroides sp017561765	79.5857	176	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017554335.1	s__Cryptobacteroides sp017554335	79.4915	197	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017551425.1	s__Cryptobacteroides sp017551425	79.2929	130	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017616595.1	s__Cryptobacteroides sp017616595	79.1283	148	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017615615.1	s__Cryptobacteroides sp017615615	78.8909	122	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 17:04:15,666] [INFO] GTDB search result was written to GCA_017448655.1_ASM1744865v1_genomic.fna/result_gtdb.tsv
[2023-06-28 17:04:15,666] [INFO] ===== GTDB Search completed =====
[2023-06-28 17:04:15,669] [INFO] DFAST_QC result json was written to GCA_017448655.1_ASM1744865v1_genomic.fna/dqc_result.json
[2023-06-28 17:04:15,670] [INFO] DFAST_QC completed!
[2023-06-28 17:04:15,670] [INFO] Total running time: 0h1m14s