[2023-03-16 08:22:25,416] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:22:25,418] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:22:25,418] [INFO] DQC Reference Directory: /var/lib/cwl/stg663222b2-9bd3-47ba-ae85-d0460c1e72e0/dqc_reference
[2023-03-16 08:22:27,104] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:22:27,104] [INFO] Task started: Prodigal
[2023-03-16 08:22:27,104] [INFO] Running command: cat /var/lib/cwl/stg91d8078b-46dc-46b7-b5ab-7a084d029ba2/OceanDNA-b2203.fa | prodigal -d OceanDNA-b2203/cds.fna -a OceanDNA-b2203/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:22:30,783] [INFO] Task succeeded: Prodigal
[2023-03-16 08:22:30,784] [INFO] Task started: HMMsearch
[2023-03-16 08:22:30,784] [INFO] Running command: hmmsearch --tblout OceanDNA-b2203/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg663222b2-9bd3-47ba-ae85-d0460c1e72e0/dqc_reference/reference_markers.hmm OceanDNA-b2203/protein.faa > /dev/null
[2023-03-16 08:22:30,932] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:22:30,932] [INFO] Found 6/6 markers.
[2023-03-16 08:22:30,946] [INFO] Query marker FASTA was written to OceanDNA-b2203/markers.fasta
[2023-03-16 08:22:30,947] [INFO] Task started: Blastn
[2023-03-16 08:22:30,947] [INFO] Running command: blastn -query OceanDNA-b2203/markers.fasta -db /var/lib/cwl/stg663222b2-9bd3-47ba-ae85-d0460c1e72e0/dqc_reference/reference_markers.fasta -out OceanDNA-b2203/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:22:32,578] [INFO] Task succeeded: Blastn
[2023-03-16 08:22:32,584] [INFO] Selected 12 target genomes.
[2023-03-16 08:22:32,585] [INFO] Target genome list was writen to OceanDNA-b2203/target_genomes.txt
[2023-03-16 08:22:32,591] [INFO] Task started: fastANI
[2023-03-16 08:22:32,591] [INFO] Running command: fastANI --query /var/lib/cwl/stg91d8078b-46dc-46b7-b5ab-7a084d029ba2/OceanDNA-b2203.fa --refList OceanDNA-b2203/target_genomes.txt --output OceanDNA-b2203/fastani_result.tsv --threads 1
[2023-03-16 08:22:36,393] [INFO] Task succeeded: fastANI
[2023-03-16 08:22:36,393] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg663222b2-9bd3-47ba-ae85-d0460c1e72e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:22:36,394] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg663222b2-9bd3-47ba-ae85-d0460c1e72e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:22:36,394] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:22:36,394] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 08:22:36,394] [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
--------------------------------------------------------------------------------
[2023-03-16 08:22:36,396] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2203/tc_result.tsv
[2023-03-16 08:22:36,398] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:22:36,398] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:22:36,398] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg663222b2-9bd3-47ba-ae85-d0460c1e72e0/dqc_reference/checkm_data
[2023-03-16 08:22:36,408] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:22:36,595] [INFO] Task started: CheckM
[2023-03-16 08:22:36,595] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2203/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2203/checkm_input OceanDNA-b2203/checkm_result
[2023-03-16 08:22:53,953] [INFO] Task succeeded: CheckM
[2023-03-16 08:22:53,953] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 2.23%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 08:22:53,973] [INFO] ===== Completeness check finished =====
[2023-03-16 08:22:53,973] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:22:53,973] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2203/markers.fasta)
[2023-03-16 08:22:53,975] [INFO] Task started: Blastn
[2023-03-16 08:22:53,975] [INFO] Running command: blastn -query OceanDNA-b2203/markers.fasta -db /var/lib/cwl/stg663222b2-9bd3-47ba-ae85-d0460c1e72e0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2203/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:22:54,687] [INFO] Task succeeded: Blastn
[2023-03-16 08:22:54,689] [INFO] Selected 16 target genomes.
[2023-03-16 08:22:54,689] [INFO] Target genome list was writen to OceanDNA-b2203/target_genomes_gtdb.txt
[2023-03-16 08:22:54,709] [INFO] Task started: fastANI
[2023-03-16 08:22:54,709] [INFO] Running command: fastANI --query /var/lib/cwl/stg91d8078b-46dc-46b7-b5ab-7a084d029ba2/OceanDNA-b2203.fa --refList OceanDNA-b2203/target_genomes_gtdb.txt --output OceanDNA-b2203/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:22:57,530] [INFO] Task succeeded: fastANI
[2023-03-16 08:22:57,539] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 08:22:57,540] [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_902593795.1	s__Actinomarina sp902593795	85.2308	200	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	84.6249	200	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_004213405.1	s__Actinomarina sp004213405	82.1548	122	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_902610815.1	s__Actinomarina sp902610815	81.9118	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_902580215.1	s__Actinomarina sp902580215	81.5757	170	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_902599555.1	s__Actinomarina sp902599555	81.5603	162	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_016777845.1	s__Actinomarina sp016777845	81.5307	133	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	80.878	173	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	79.7327	89	240	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	97.26	97.26	0.73	0.73	2	-
GCA_003281085.1	s__Actinomarina sp003281085	79.4975	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_902596545.1	s__Actinomarina sp902596545	79.1453	101	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_003213165.1	s__Actinomarina sp003213165	78.8963	93	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_902625455.1	s__Actinomarina sp902625455	78.7026	107	240	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	97.46	97.35	0.85	0.81	4	-
GCA_003282445.1	s__Actinomarina sp003282445	77.1548	67	240	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	97.01	96.02	0.90	0.85	11	-
GCA_014384285.1	s__Actinomarina sp014384285	77.1466	55	240	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	99.05	98.78	0.90	0.82	4	-
--------------------------------------------------------------------------------
[2023-03-16 08:22:57,540] [INFO] GTDB search result was written to OceanDNA-b2203/result_gtdb.tsv
[2023-03-16 08:22:57,540] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:22:57,542] [INFO] DFAST_QC result json was written to OceanDNA-b2203/dqc_result.json
[2023-03-16 08:22:57,542] [INFO] DFAST_QC completed!
[2023-03-16 08:22:57,542] [INFO] Total running time: 0h0m32s