[2023-03-14 11:33:34,904] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:33:34,904] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:33:34,904] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d23372a-ca58-45ba-8594-eef07598b014/dqc_reference
[2023-03-14 11:33:36,061] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:33:36,061] [INFO] Task started: Prodigal
[2023-03-14 11:33:36,061] [INFO] Running command: cat /var/lib/cwl/stgbe16b000-03fd-46bb-9ff5-74ec2c617eca/OceanDNA-b17719.fa | prodigal -d OceanDNA-b17719/cds.fna -a OceanDNA-b17719/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:34:07,995] [INFO] Task succeeded: Prodigal
[2023-03-14 11:34:07,995] [INFO] Task started: HMMsearch
[2023-03-14 11:34:07,995] [INFO] Running command: hmmsearch --tblout OceanDNA-b17719/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d23372a-ca58-45ba-8594-eef07598b014/dqc_reference/reference_markers.hmm OceanDNA-b17719/protein.faa > /dev/null
[2023-03-14 11:34:08,249] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:34:08,250] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgbe16b000-03fd-46bb-9ff5-74ec2c617eca/OceanDNA-b17719.fa]
[2023-03-14 11:34:08,283] [INFO] Query marker FASTA was written to OceanDNA-b17719/markers.fasta
[2023-03-14 11:34:08,283] [INFO] Task started: Blastn
[2023-03-14 11:34:08,283] [INFO] Running command: blastn -query OceanDNA-b17719/markers.fasta -db /var/lib/cwl/stg0d23372a-ca58-45ba-8594-eef07598b014/dqc_reference/reference_markers.fasta -out OceanDNA-b17719/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:34:08,831] [INFO] Task succeeded: Blastn
[2023-03-14 11:34:08,831] [INFO] Selected 27 target genomes.
[2023-03-14 11:34:08,832] [INFO] Target genome list was writen to OceanDNA-b17719/target_genomes.txt
[2023-03-14 11:34:08,847] [INFO] Task started: fastANI
[2023-03-14 11:34:08,847] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe16b000-03fd-46bb-9ff5-74ec2c617eca/OceanDNA-b17719.fa --refList OceanDNA-b17719/target_genomes.txt --output OceanDNA-b17719/fastani_result.tsv --threads 1
[2023-03-14 11:34:27,892] [INFO] Task succeeded: fastANI
[2023-03-14 11:34:27,892] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d23372a-ca58-45ba-8594-eef07598b014/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:34:27,892] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d23372a-ca58-45ba-8594-eef07598b014/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:34:27,895] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:34:27,895] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 11:34:27,895] [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
Archangium violaceum	strain=Cb vi76	GCA_000733295.1	83451	83451	type	True	74.8443	57	1754	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 11:34:27,895] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17719/tc_result.tsv
[2023-03-14 11:34:27,895] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:34:27,895] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:34:27,895] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d23372a-ca58-45ba-8594-eef07598b014/dqc_reference/checkm_data
[2023-03-14 11:34:27,896] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:34:28,094] [INFO] Task started: CheckM
[2023-03-14 11:34:28,094] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17719/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17719/checkm_input OceanDNA-b17719/checkm_result
[2023-03-14 11:35:43,205] [INFO] Task succeeded: CheckM
[2023-03-14 11:35:43,205] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:35:43,209] [INFO] ===== Completeness check finished =====
[2023-03-14 11:35:43,209] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:35:43,209] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17719/markers.fasta)
[2023-03-14 11:35:43,210] [INFO] Task started: Blastn
[2023-03-14 11:35:43,210] [INFO] Running command: blastn -query OceanDNA-b17719/markers.fasta -db /var/lib/cwl/stg0d23372a-ca58-45ba-8594-eef07598b014/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17719/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:35:43,948] [INFO] Task succeeded: Blastn
[2023-03-14 11:35:43,949] [INFO] Selected 24 target genomes.
[2023-03-14 11:35:43,949] [INFO] Target genome list was writen to OceanDNA-b17719/target_genomes_gtdb.txt
[2023-03-14 11:35:44,027] [INFO] Task started: fastANI
[2023-03-14 11:35:44,027] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe16b000-03fd-46bb-9ff5-74ec2c617eca/OceanDNA-b17719.fa --refList OceanDNA-b17719/target_genomes_gtdb.txt --output OceanDNA-b17719/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:35:59,319] [INFO] Task succeeded: fastANI
[2023-03-14 11:35:59,324] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:35:59,324] [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_002725915.1	s__GCA-2725915 sp002725915	83.4238	742	1754	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2725915	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018660835.1	s__UBA12574 sp018660835	76.4024	75	1754	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__UBA12574	95.0	99.93	99.91	0.98	0.97	7	-
GCA_002726335.1	s__UBA8231 sp002726335	76.1171	158	1754	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__UBA8231	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015660315.1	s__GCA-2724215 sp015660315	76.0503	55	1754	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002712305.1	s__UBA12574 sp002712305	75.7273	80	1754	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__UBA12574	95.0	98.27	97.81	0.83	0.79	3	-
GCA_016187725.1	s__SICG01 sp016187725	75.7247	148	1754	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__SICG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009691525.1	s__SICG01 sp009691525	75.5839	115	1754	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__SICG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:35:59,325] [INFO] GTDB search result was written to OceanDNA-b17719/result_gtdb.tsv
[2023-03-14 11:35:59,325] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:35:59,326] [INFO] DFAST_QC result json was written to OceanDNA-b17719/dqc_result.json
[2023-03-14 11:35:59,326] [INFO] DFAST_QC completed!
[2023-03-14 11:35:59,326] [INFO] Total running time: 0h2m24s