[2023-03-17 11:57:19,286] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:57:19,286] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:57:19,286] [INFO] DQC Reference Directory: /var/lib/cwl/stgb768cd63-1f42-4e29-b21b-86dbb5174c09/dqc_reference
[2023-03-17 11:57:20,887] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:57:20,888] [INFO] Task started: Prodigal
[2023-03-17 11:57:20,888] [INFO] Running command: cat /var/lib/cwl/stg1d5b043f-d5df-47e8-965f-4c8834cdc620/OceanDNA-b14328.fa | prodigal -d OceanDNA-b14328/cds.fna -a OceanDNA-b14328/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:57:30,501] [INFO] Task succeeded: Prodigal
[2023-03-17 11:57:30,502] [INFO] Task started: HMMsearch
[2023-03-17 11:57:30,502] [INFO] Running command: hmmsearch --tblout OceanDNA-b14328/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb768cd63-1f42-4e29-b21b-86dbb5174c09/dqc_reference/reference_markers.hmm OceanDNA-b14328/protein.faa > /dev/null
[2023-03-17 11:57:30,670] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:57:30,671] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1d5b043f-d5df-47e8-965f-4c8834cdc620/OceanDNA-b14328.fa]
[2023-03-17 11:57:30,682] [INFO] Query marker FASTA was written to OceanDNA-b14328/markers.fasta
[2023-03-17 11:57:30,682] [INFO] Task started: Blastn
[2023-03-17 11:57:30,682] [INFO] Running command: blastn -query OceanDNA-b14328/markers.fasta -db /var/lib/cwl/stgb768cd63-1f42-4e29-b21b-86dbb5174c09/dqc_reference/reference_markers.fasta -out OceanDNA-b14328/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:57:31,165] [INFO] Task succeeded: Blastn
[2023-03-17 11:57:31,165] [INFO] Selected 8 target genomes.
[2023-03-17 11:57:31,166] [INFO] Target genome list was writen to OceanDNA-b14328/target_genomes.txt
[2023-03-17 11:57:31,171] [INFO] Task started: fastANI
[2023-03-17 11:57:31,171] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d5b043f-d5df-47e8-965f-4c8834cdc620/OceanDNA-b14328.fa --refList OceanDNA-b14328/target_genomes.txt --output OceanDNA-b14328/fastani_result.tsv --threads 1
[2023-03-17 11:57:34,734] [INFO] Task succeeded: fastANI
[2023-03-17 11:57:34,735] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb768cd63-1f42-4e29-b21b-86dbb5174c09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:57:34,735] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb768cd63-1f42-4e29-b21b-86dbb5174c09/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:57:34,735] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:57:34,735] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 11:57:34,735] [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
--------------------------------------------------------------------------------
[2023-03-17 11:57:34,735] [INFO] DFAST Taxonomy check result was written to OceanDNA-b14328/tc_result.tsv
[2023-03-17 11:57:34,735] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:57:34,735] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:57:34,736] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb768cd63-1f42-4e29-b21b-86dbb5174c09/dqc_reference/checkm_data
[2023-03-17 11:57:34,738] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:57:34,741] [INFO] Task started: CheckM
[2023-03-17 11:57:34,741] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b14328/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b14328/checkm_input OceanDNA-b14328/checkm_result
[2023-03-17 11:58:03,066] [INFO] Task succeeded: CheckM
[2023-03-17 11:58:03,066] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:58:03,068] [INFO] ===== Completeness check finished =====
[2023-03-17 11:58:03,068] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:58:03,068] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b14328/markers.fasta)
[2023-03-17 11:58:03,068] [INFO] Task started: Blastn
[2023-03-17 11:58:03,069] [INFO] Running command: blastn -query OceanDNA-b14328/markers.fasta -db /var/lib/cwl/stgb768cd63-1f42-4e29-b21b-86dbb5174c09/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b14328/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:58:03,710] [INFO] Task succeeded: Blastn
[2023-03-17 11:58:03,710] [INFO] Selected 9 target genomes.
[2023-03-17 11:58:03,710] [INFO] Target genome list was writen to OceanDNA-b14328/target_genomes_gtdb.txt
[2023-03-17 11:58:03,748] [INFO] Task started: fastANI
[2023-03-17 11:58:03,749] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d5b043f-d5df-47e8-965f-4c8834cdc620/OceanDNA-b14328.fa --refList OceanDNA-b14328/target_genomes_gtdb.txt --output OceanDNA-b14328/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:58:06,645] [INFO] Task succeeded: fastANI
[2023-03-17 11:58:06,650] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 11:58:06,651] [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_002722155.1	s__UBA11996 sp002722155	99.649	470	582	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__UBA11996	95.0	99.59	99.59	0.67	0.67	2	conclusive
GCA_008373095.1	s__UBA11996 sp002320875	83.3147	319	582	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__UBA11996	95.0	99.51	99.45	0.90	0.90	3	-
GCA_002728195.1	s__UBA11996 sp002728195	80.3301	256	582	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__UBA11996	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002500485.1	s__UBA11996 sp002500485	77.673	159	582	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__UBA11996	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012965485.1	s__UBA11996 sp012965485	77.1632	77	582	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__UBA11996	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002435305.1	s__UBA11996 sp002435305	76.9378	153	582	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__UBA11996	95.0	99.14	98.93	0.85	0.82	4	-
GCA_003228105.1	s__UBA11996 sp003228105	76.9113	131	582	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SAR202;f__UBA826;g__UBA11996	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 11:58:06,651] [INFO] GTDB search result was written to OceanDNA-b14328/result_gtdb.tsv
[2023-03-17 11:58:06,651] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:58:06,652] [INFO] DFAST_QC result json was written to OceanDNA-b14328/dqc_result.json
[2023-03-17 11:58:06,652] [INFO] DFAST_QC completed!
[2023-03-17 11:58:06,652] [INFO] Total running time: 0h0m47s