[2023-06-28 23:18:31,203] [INFO] DFAST_QC pipeline started.
[2023-06-28 23:18:31,209] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 23:18:31,209] [INFO] DQC Reference Directory: /var/lib/cwl/stg1a8c9ce9-c506-4e47-9387-d6035ac52dad/dqc_reference
[2023-06-28 23:18:33,588] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 23:18:33,589] [INFO] Task started: Prodigal
[2023-06-28 23:18:33,590] [INFO] Running command: gunzip -c /var/lib/cwl/stg558f1a80-7934-4cd4-b4ad-ab6bbdc4d9b9/GCA_017964005.1_ASM1796400v1_genomic.fna.gz | prodigal -d GCA_017964005.1_ASM1796400v1_genomic.fna/cds.fna -a GCA_017964005.1_ASM1796400v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 23:18:39,402] [INFO] Task succeeded: Prodigal
[2023-06-28 23:18:39,403] [INFO] Task started: HMMsearch
[2023-06-28 23:18:39,403] [INFO] Running command: hmmsearch --tblout GCA_017964005.1_ASM1796400v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1a8c9ce9-c506-4e47-9387-d6035ac52dad/dqc_reference/reference_markers.hmm GCA_017964005.1_ASM1796400v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 23:18:39,624] [INFO] Task succeeded: HMMsearch
[2023-06-28 23:18:39,626] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg558f1a80-7934-4cd4-b4ad-ab6bbdc4d9b9/GCA_017964005.1_ASM1796400v1_genomic.fna.gz]
[2023-06-28 23:18:39,653] [INFO] Query marker FASTA was written to GCA_017964005.1_ASM1796400v1_genomic.fna/markers.fasta
[2023-06-28 23:18:39,653] [INFO] Task started: Blastn
[2023-06-28 23:18:39,653] [INFO] Running command: blastn -query GCA_017964005.1_ASM1796400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a8c9ce9-c506-4e47-9387-d6035ac52dad/dqc_reference/reference_markers.fasta -out GCA_017964005.1_ASM1796400v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:18:40,248] [INFO] Task succeeded: Blastn
[2023-06-28 23:18:40,253] [INFO] Selected 19 target genomes.
[2023-06-28 23:18:40,253] [INFO] Target genome list was writen to GCA_017964005.1_ASM1796400v1_genomic.fna/target_genomes.txt
[2023-06-28 23:18:40,259] [INFO] Task started: fastANI
[2023-06-28 23:18:40,259] [INFO] Running command: fastANI --query /var/lib/cwl/stg558f1a80-7934-4cd4-b4ad-ab6bbdc4d9b9/GCA_017964005.1_ASM1796400v1_genomic.fna.gz --refList GCA_017964005.1_ASM1796400v1_genomic.fna/target_genomes.txt --output GCA_017964005.1_ASM1796400v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 23:18:51,064] [INFO] Task succeeded: fastANI
[2023-06-28 23:18:51,065] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1a8c9ce9-c506-4e47-9387-d6035ac52dad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 23:18:51,065] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1a8c9ce9-c506-4e47-9387-d6035ac52dad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 23:18:51,067] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 23:18:51,067] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 23:18:51,068] [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 23:18:51,070] [INFO] DFAST Taxonomy check result was written to GCA_017964005.1_ASM1796400v1_genomic.fna/tc_result.tsv
[2023-06-28 23:18:51,071] [INFO] ===== Taxonomy check completed =====
[2023-06-28 23:18:51,071] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 23:18:51,071] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1a8c9ce9-c506-4e47-9387-d6035ac52dad/dqc_reference/checkm_data
[2023-06-28 23:18:51,076] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 23:18:51,111] [INFO] Task started: CheckM
[2023-06-28 23:18:51,111] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017964005.1_ASM1796400v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017964005.1_ASM1796400v1_genomic.fna/checkm_input GCA_017964005.1_ASM1796400v1_genomic.fna/checkm_result
[2023-06-28 23:19:15,062] [INFO] Task succeeded: CheckM
[2023-06-28 23:19:15,063] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 23:19:15,085] [INFO] ===== Completeness check finished =====
[2023-06-28 23:19:15,085] [INFO] ===== Start GTDB Search =====
[2023-06-28 23:19:15,086] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017964005.1_ASM1796400v1_genomic.fna/markers.fasta)
[2023-06-28 23:19:15,086] [INFO] Task started: Blastn
[2023-06-28 23:19:15,086] [INFO] Running command: blastn -query GCA_017964005.1_ASM1796400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1a8c9ce9-c506-4e47-9387-d6035ac52dad/dqc_reference/reference_markers_gtdb.fasta -out GCA_017964005.1_ASM1796400v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 23:19:15,950] [INFO] Task succeeded: Blastn
[2023-06-28 23:19:15,955] [INFO] Selected 15 target genomes.
[2023-06-28 23:19:15,955] [INFO] Target genome list was writen to GCA_017964005.1_ASM1796400v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 23:19:15,979] [INFO] Task started: fastANI
[2023-06-28 23:19:15,979] [INFO] Running command: fastANI --query /var/lib/cwl/stg558f1a80-7934-4cd4-b4ad-ab6bbdc4d9b9/GCA_017964005.1_ASM1796400v1_genomic.fna.gz --refList GCA_017964005.1_ASM1796400v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017964005.1_ASM1796400v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 23:19:23,098] [INFO] Task succeeded: fastANI
[2023-06-28 23:19:23,110] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 23:19:23,110] [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_017964005.1	s__Saccharofermentans sp017964005	100.0	789	789	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Saccharofermentans	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017615325.1	s__Saccharofermentans sp017615325	81.645	385	789	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Saccharofermentans	95.0	97.21	97.21	0.83	0.83	2	-
GCA_016292135.1	s__Saccharofermentans sp016292135	80.77	384	789	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Saccharofermentans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902782125.1	s__Saccharofermentans sp902782125	78.0751	113	789	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Saccharofermentans	95.0	96.57	95.78	0.89	0.85	10	-
GCA_017427465.1	s__Saccharofermentans sp017427465	78.0655	90	789	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Saccharofermentans	95.0	97.19	97.19	0.90	0.90	2	-
GCA_017428155.1	s__Saccharofermentans sp017428155	77.893	132	789	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Saccharofermentans	95.0	97.63	97.45	0.90	0.89	3	-
GCA_017550385.1	s__Saccharofermentans sp017550385	77.8587	91	789	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Saccharofermentans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017529925.1	s__Saccharofermentans sp017529925	77.8379	87	789	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Saccharofermentans	95.0	98.07	97.80	0.94	0.92	4	-
GCA_900111435.1	s__Saccharofermentans sp900111435	77.6929	88	789	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Saccharofermentans	95.0	98.11	97.94	0.95	0.93	7	-
GCA_902801755.1	s__Saccharofermentans sp902801755	77.6917	102	789	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Saccharofermentans	95.0	98.05	98.05	0.82	0.82	2	-
GCA_902788505.1	s__Saccharofermentans sp902788505	77.6762	101	789	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Saccharofermentans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902789515.1	s__Saccharofermentans sp902789515	77.4631	92	789	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Saccharofermentans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002450155.1	s__Saccharofermentans sp002450155	77.4306	84	789	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Saccharofermentans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902776845.1	s__Saccharofermentans sp902776845	77.2681	102	789	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Saccharofermentanales;f__Saccharofermentanaceae;g__Saccharofermentans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 23:19:23,112] [INFO] GTDB search result was written to GCA_017964005.1_ASM1796400v1_genomic.fna/result_gtdb.tsv
[2023-06-28 23:19:23,113] [INFO] ===== GTDB Search completed =====
[2023-06-28 23:19:23,116] [INFO] DFAST_QC result json was written to GCA_017964005.1_ASM1796400v1_genomic.fna/dqc_result.json
[2023-06-28 23:19:23,116] [INFO] DFAST_QC completed!
[2023-06-28 23:19:23,116] [INFO] Total running time: 0h0m52s