[2023-03-15 04:01:38,401] [INFO] DFAST_QC pipeline started.
[2023-03-15 04:01:38,401] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 04:01:38,401] [INFO] DQC Reference Directory: /var/lib/cwl/stg53e21818-c7fa-49a9-8219-76f2fd481d8d/dqc_reference
[2023-03-15 04:01:39,478] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 04:01:39,479] [INFO] Task started: Prodigal
[2023-03-15 04:01:39,479] [INFO] Running command: cat /var/lib/cwl/stged82ce1b-ec2a-4d44-bf42-d02a9363f23c/OceanDNA-b2156.fa | prodigal -d OceanDNA-b2156/cds.fna -a OceanDNA-b2156/protein.faa -g 11 -q > /dev/null
[2023-03-15 04:01:43,252] [INFO] Task succeeded: Prodigal
[2023-03-15 04:01:43,253] [INFO] Task started: HMMsearch
[2023-03-15 04:01:43,253] [INFO] Running command: hmmsearch --tblout OceanDNA-b2156/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53e21818-c7fa-49a9-8219-76f2fd481d8d/dqc_reference/reference_markers.hmm OceanDNA-b2156/protein.faa > /dev/null
[2023-03-15 04:01:43,396] [INFO] Task succeeded: HMMsearch
[2023-03-15 04:01:43,396] [INFO] Found 6/6 markers.
[2023-03-15 04:01:43,406] [INFO] Query marker FASTA was written to OceanDNA-b2156/markers.fasta
[2023-03-15 04:01:43,408] [INFO] Task started: Blastn
[2023-03-15 04:01:43,408] [INFO] Running command: blastn -query OceanDNA-b2156/markers.fasta -db /var/lib/cwl/stg53e21818-c7fa-49a9-8219-76f2fd481d8d/dqc_reference/reference_markers.fasta -out OceanDNA-b2156/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:01:43,993] [INFO] Task succeeded: Blastn
[2023-03-15 04:01:43,995] [INFO] Selected 9 target genomes.
[2023-03-15 04:01:43,995] [INFO] Target genome list was writen to OceanDNA-b2156/target_genomes.txt
[2023-03-15 04:01:44,006] [INFO] Task started: fastANI
[2023-03-15 04:01:44,006] [INFO] Running command: fastANI --query /var/lib/cwl/stged82ce1b-ec2a-4d44-bf42-d02a9363f23c/OceanDNA-b2156.fa --refList OceanDNA-b2156/target_genomes.txt --output OceanDNA-b2156/fastani_result.tsv --threads 1
[2023-03-15 04:01:48,957] [INFO] Task succeeded: fastANI
[2023-03-15 04:01:48,957] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53e21818-c7fa-49a9-8219-76f2fd481d8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 04:01:48,957] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53e21818-c7fa-49a9-8219-76f2fd481d8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 04:01:48,957] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 04:01:48,957] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 04:01:48,958] [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
--------------------------------------------------------------------------------
[2023-03-15 04:01:48,958] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2156/tc_result.tsv
[2023-03-15 04:01:48,958] [INFO] ===== Taxonomy check completed =====
[2023-03-15 04:01:48,958] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 04:01:48,958] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53e21818-c7fa-49a9-8219-76f2fd481d8d/dqc_reference/checkm_data
[2023-03-15 04:01:48,961] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 04:01:48,964] [INFO] Task started: CheckM
[2023-03-15 04:01:48,964] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2156/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2156/checkm_input OceanDNA-b2156/checkm_result
[2023-03-15 04:02:05,101] [INFO] Task succeeded: CheckM
[2023-03-15 04:02:05,102] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 04:02:05,109] [INFO] ===== Completeness check finished =====
[2023-03-15 04:02:05,110] [INFO] ===== Start GTDB Search =====
[2023-03-15 04:02:05,110] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2156/markers.fasta)
[2023-03-15 04:02:05,111] [INFO] Task started: Blastn
[2023-03-15 04:02:05,111] [INFO] Running command: blastn -query OceanDNA-b2156/markers.fasta -db /var/lib/cwl/stg53e21818-c7fa-49a9-8219-76f2fd481d8d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2156/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 04:02:06,130] [INFO] Task succeeded: Blastn
[2023-03-15 04:02:06,132] [INFO] Selected 24 target genomes.
[2023-03-15 04:02:06,132] [INFO] Target genome list was writen to OceanDNA-b2156/target_genomes_gtdb.txt
[2023-03-15 04:02:06,147] [INFO] Task started: fastANI
[2023-03-15 04:02:06,147] [INFO] Running command: fastANI --query /var/lib/cwl/stged82ce1b-ec2a-4d44-bf42-d02a9363f23c/OceanDNA-b2156.fa --refList OceanDNA-b2156/target_genomes_gtdb.txt --output OceanDNA-b2156/fastani_result_gtdb.tsv --threads 1
[2023-03-15 04:02:11,088] [INFO] Task succeeded: fastANI
[2023-03-15 04:02:11,098] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 04:02:11,098] [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_902521955.1	s__Actinomarina sp902521955	88.9898	176	240	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902519215.1	s__Actinomarina sp902519215	87.533	182	240	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	96.27	96.27	0.84	0.84	2	-
GCA_902555055.1	s__Actinomarina sp902555055	86.9774	180	240	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902593795.1	s__Actinomarina sp902593795	79.1864	106	240	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	97.69	97.47	0.86	0.85	3	-
GCA_902555985.1	s__Actinomarina sp902555985	79.0981	110	240	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	97.40	96.59	0.85	0.83	4	-
GCA_902610815.1	s__Actinomarina sp902610815	78.8749	101	240	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902596545.1	s__Actinomarina sp902596545	78.7954	111	240	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	98.42	98.42	0.93	0.93	2	-
GCA_016777845.1	s__Actinomarina sp016777845	78.775	75	240	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902622665.1	s__Actinomarina sp902622665	78.765	88	240	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003213165.1	s__Actinomarina sp003213165	78.6995	97	240	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	97.69	95.56	0.85	0.73	10	-
GCA_902599555.1	s__Actinomarina sp902599555	78.6787	92	240	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902580215.1	s__Actinomarina sp902580215	78.6694	103	240	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	95.48	95.05	0.79	0.77	5	-
GCA_902576605.1	s__Actinomarina sp902576605	78.5991	73	240	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003281085.1	s__Actinomarina sp003281085	78.507	97	240	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	96.17	95.08	0.82	0.73	10	-
GCA_902628045.1	s__Actinomarina sp902628045	78.4015	81	240	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902595195.1	s__Actinomarina sp902595195	78.396	92	240	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	97.26	97.26	0.73	0.73	2	-
--------------------------------------------------------------------------------
[2023-03-15 04:02:11,099] [INFO] GTDB search result was written to OceanDNA-b2156/result_gtdb.tsv
[2023-03-15 04:02:11,100] [INFO] ===== GTDB Search completed =====
[2023-03-15 04:02:11,102] [INFO] DFAST_QC result json was written to OceanDNA-b2156/dqc_result.json
[2023-03-15 04:02:11,103] [INFO] DFAST_QC completed!
[2023-03-15 04:02:11,103] [INFO] Total running time: 0h0m33s