[2023-06-27 05:00:03,246] [INFO] DFAST_QC pipeline started.
[2023-06-27 05:00:03,249] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 05:00:03,249] [INFO] DQC Reference Directory: /var/lib/cwl/stg58e32b29-e7e4-4894-b865-a82cc372db3f/dqc_reference
[2023-06-27 05:00:06,119] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 05:00:06,120] [INFO] Task started: Prodigal
[2023-06-27 05:00:06,120] [INFO] Running command: gunzip -c /var/lib/cwl/stg931fd481-63ca-4abc-8fa9-08f2b4927af5/GCA_002310175.1_ASM231017v1_genomic.fna.gz | prodigal -d GCA_002310175.1_ASM231017v1_genomic.fna/cds.fna -a GCA_002310175.1_ASM231017v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 05:00:16,979] [INFO] Task succeeded: Prodigal
[2023-06-27 05:00:16,980] [INFO] Task started: HMMsearch
[2023-06-27 05:00:16,980] [INFO] Running command: hmmsearch --tblout GCA_002310175.1_ASM231017v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58e32b29-e7e4-4894-b865-a82cc372db3f/dqc_reference/reference_markers.hmm GCA_002310175.1_ASM231017v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 05:00:17,168] [INFO] Task succeeded: HMMsearch
[2023-06-27 05:00:17,170] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg931fd481-63ca-4abc-8fa9-08f2b4927af5/GCA_002310175.1_ASM231017v1_genomic.fna.gz]
[2023-06-27 05:00:17,193] [INFO] Query marker FASTA was written to GCA_002310175.1_ASM231017v1_genomic.fna/markers.fasta
[2023-06-27 05:00:17,194] [INFO] Task started: Blastn
[2023-06-27 05:00:17,194] [INFO] Running command: blastn -query GCA_002310175.1_ASM231017v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58e32b29-e7e4-4894-b865-a82cc372db3f/dqc_reference/reference_markers.fasta -out GCA_002310175.1_ASM231017v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:00:17,748] [INFO] Task succeeded: Blastn
[2023-06-27 05:00:17,751] [INFO] Selected 21 target genomes.
[2023-06-27 05:00:17,752] [INFO] Target genome list was writen to GCA_002310175.1_ASM231017v1_genomic.fna/target_genomes.txt
[2023-06-27 05:00:17,758] [INFO] Task started: fastANI
[2023-06-27 05:00:17,758] [INFO] Running command: fastANI --query /var/lib/cwl/stg931fd481-63ca-4abc-8fa9-08f2b4927af5/GCA_002310175.1_ASM231017v1_genomic.fna.gz --refList GCA_002310175.1_ASM231017v1_genomic.fna/target_genomes.txt --output GCA_002310175.1_ASM231017v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 05:00:32,027] [INFO] Task succeeded: fastANI
[2023-06-27 05:00:32,027] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58e32b29-e7e4-4894-b865-a82cc372db3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 05:00:32,028] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58e32b29-e7e4-4894-b865-a82cc372db3f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 05:00:32,029] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 05:00:32,029] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 05:00:32,029] [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
--------------------------------------------------------------------------------
[2023-06-27 05:00:32,031] [INFO] DFAST Taxonomy check result was written to GCA_002310175.1_ASM231017v1_genomic.fna/tc_result.tsv
[2023-06-27 05:00:32,033] [INFO] ===== Taxonomy check completed =====
[2023-06-27 05:00:32,033] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 05:00:32,033] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58e32b29-e7e4-4894-b865-a82cc372db3f/dqc_reference/checkm_data
[2023-06-27 05:00:32,036] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 05:00:32,063] [INFO] Task started: CheckM
[2023-06-27 05:00:32,063] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002310175.1_ASM231017v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002310175.1_ASM231017v1_genomic.fna/checkm_input GCA_002310175.1_ASM231017v1_genomic.fna/checkm_result
[2023-06-27 05:01:07,867] [INFO] Task succeeded: CheckM
[2023-06-27 05:01:07,868] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 05:01:07,887] [INFO] ===== Completeness check finished =====
[2023-06-27 05:01:07,888] [INFO] ===== Start GTDB Search =====
[2023-06-27 05:01:07,888] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002310175.1_ASM231017v1_genomic.fna/markers.fasta)
[2023-06-27 05:01:07,888] [INFO] Task started: Blastn
[2023-06-27 05:01:07,888] [INFO] Running command: blastn -query GCA_002310175.1_ASM231017v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58e32b29-e7e4-4894-b865-a82cc372db3f/dqc_reference/reference_markers_gtdb.fasta -out GCA_002310175.1_ASM231017v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 05:01:08,664] [INFO] Task succeeded: Blastn
[2023-06-27 05:01:08,692] [INFO] Selected 16 target genomes.
[2023-06-27 05:01:08,692] [INFO] Target genome list was writen to GCA_002310175.1_ASM231017v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 05:01:08,700] [INFO] Task started: fastANI
[2023-06-27 05:01:08,700] [INFO] Running command: fastANI --query /var/lib/cwl/stg931fd481-63ca-4abc-8fa9-08f2b4927af5/GCA_002310175.1_ASM231017v1_genomic.fna.gz --refList GCA_002310175.1_ASM231017v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002310175.1_ASM231017v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 05:01:16,305] [INFO] Task succeeded: fastANI
[2023-06-27 05:01:16,319] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 05:01:16,319] [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_002310175.1	s__UBA1179 sp002310175	100.0	672	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017651315.1	s__UBA1179 sp017651315	84.6535	456	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	97.72	97.72	0.81	0.81	2	-
GCA_900318995.1	s__UBA1179 sp900318995	82.1259	315	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	96.89	96.18	0.89	0.85	8	-
GCA_902782245.1	s__UBA1179 sp902782245	82.1209	305	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	96.81	95.66	0.89	0.85	3	-
GCA_017530735.1	s__UBA1179 sp017530735	81.3278	280	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	98.35	98.35	0.83	0.83	2	-
GCA_017612875.1	s__UBA1179 sp017612875	81.0007	285	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902799685.1	s__UBA1179 sp902799685	80.8281	328	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	96.39	96.39	0.82	0.82	2	-
GCA_017642425.1	s__UBA1179 sp017642425	80.3072	297	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902763885.1	s__UBA1179 sp902763885	80.3035	276	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905234745.1	s__UBA1179 sp905234745	80.151	277	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319225.1	s__UBA1179 sp900319225	80.0823	273	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	98.54	97.96	0.93	0.90	5	-
GCA_902760965.1	s__UBA1179 sp902760965	79.9374	251	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	97.44	97.44	0.87	0.87	2	-
GCA_002309915.1	s__UBA1179 sp002309915	79.9225	219	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002310015.1	s__UBA1179 sp002310015	79.8566	253	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902774275.1	s__UBA1179 sp902774275	79.7509	237	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017551925.1	s__UBA1179 sp017551925	79.5634	252	673	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 05:01:16,321] [INFO] GTDB search result was written to GCA_002310175.1_ASM231017v1_genomic.fna/result_gtdb.tsv
[2023-06-27 05:01:16,321] [INFO] ===== GTDB Search completed =====
[2023-06-27 05:01:16,330] [INFO] DFAST_QC result json was written to GCA_002310175.1_ASM231017v1_genomic.fna/dqc_result.json
[2023-06-27 05:01:16,330] [INFO] DFAST_QC completed!
[2023-06-27 05:01:16,331] [INFO] Total running time: 0h1m13s