[2023-03-16 09:23:09,459] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:23:09,459] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:23:09,459] [INFO] DQC Reference Directory: /var/lib/cwl/stg206de88a-9c8b-44cb-b8cb-4fa54d573865/dqc_reference
[2023-03-16 09:23:11,219] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:23:11,219] [INFO] Task started: Prodigal
[2023-03-16 09:23:11,219] [INFO] Running command: cat /var/lib/cwl/stg591b09d5-98be-4874-ab1e-72d6d03138e5/OceanDNA-b14596.fa | prodigal -d OceanDNA-b14596/cds.fna -a OceanDNA-b14596/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:23:23,142] [INFO] Task succeeded: Prodigal
[2023-03-16 09:23:23,142] [INFO] Task started: HMMsearch
[2023-03-16 09:23:23,142] [INFO] Running command: hmmsearch --tblout OceanDNA-b14596/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg206de88a-9c8b-44cb-b8cb-4fa54d573865/dqc_reference/reference_markers.hmm OceanDNA-b14596/protein.faa > /dev/null
[2023-03-16 09:23:23,297] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:23:23,297] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg591b09d5-98be-4874-ab1e-72d6d03138e5/OceanDNA-b14596.fa]
[2023-03-16 09:23:23,312] [INFO] Query marker FASTA was written to OceanDNA-b14596/markers.fasta
[2023-03-16 09:23:23,312] [INFO] Task started: Blastn
[2023-03-16 09:23:23,312] [INFO] Running command: blastn -query OceanDNA-b14596/markers.fasta -db /var/lib/cwl/stg206de88a-9c8b-44cb-b8cb-4fa54d573865/dqc_reference/reference_markers.fasta -out OceanDNA-b14596/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:23:23,807] [INFO] Task succeeded: Blastn
[2023-03-16 09:23:23,808] [INFO] Selected 10 target genomes.
[2023-03-16 09:23:23,809] [INFO] Target genome list was writen to OceanDNA-b14596/target_genomes.txt
[2023-03-16 09:23:23,816] [INFO] Task started: fastANI
[2023-03-16 09:23:23,816] [INFO] Running command: fastANI --query /var/lib/cwl/stg591b09d5-98be-4874-ab1e-72d6d03138e5/OceanDNA-b14596.fa --refList OceanDNA-b14596/target_genomes.txt --output OceanDNA-b14596/fastani_result.tsv --threads 1
[2023-03-16 09:23:30,136] [INFO] Task succeeded: fastANI
[2023-03-16 09:23:30,137] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg206de88a-9c8b-44cb-b8cb-4fa54d573865/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:23:30,137] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg206de88a-9c8b-44cb-b8cb-4fa54d573865/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:23:30,137] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:23:30,137] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 09:23:30,137] [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 09:23:30,138] [INFO] DFAST Taxonomy check result was written to OceanDNA-b14596/tc_result.tsv
[2023-03-16 09:23:30,138] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:23:30,138] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:23:30,138] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg206de88a-9c8b-44cb-b8cb-4fa54d573865/dqc_reference/checkm_data
[2023-03-16 09:23:30,141] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:23:30,146] [INFO] Task started: CheckM
[2023-03-16 09:23:30,146] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b14596/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b14596/checkm_input OceanDNA-b14596/checkm_result
[2023-03-16 09:24:03,829] [INFO] Task succeeded: CheckM
[2023-03-16 09:24:03,829] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:24:03,843] [INFO] ===== Completeness check finished =====
[2023-03-16 09:24:03,843] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:24:03,843] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b14596/markers.fasta)
[2023-03-16 09:24:03,844] [INFO] Task started: Blastn
[2023-03-16 09:24:03,844] [INFO] Running command: blastn -query OceanDNA-b14596/markers.fasta -db /var/lib/cwl/stg206de88a-9c8b-44cb-b8cb-4fa54d573865/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b14596/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:24:04,518] [INFO] Task succeeded: Blastn
[2023-03-16 09:24:04,520] [INFO] Selected 11 target genomes.
[2023-03-16 09:24:04,520] [INFO] Target genome list was writen to OceanDNA-b14596/target_genomes_gtdb.txt
[2023-03-16 09:24:04,531] [INFO] Task started: fastANI
[2023-03-16 09:24:04,532] [INFO] Running command: fastANI --query /var/lib/cwl/stg591b09d5-98be-4874-ab1e-72d6d03138e5/OceanDNA-b14596.fa --refList OceanDNA-b14596/target_genomes_gtdb.txt --output OceanDNA-b14596/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:24:09,666] [INFO] Task succeeded: fastANI
[2023-03-16 09:24:09,670] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 09:24:09,670] [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_018673955.1	s__UBA1328 sp018673955	99.5236	615	678	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	99.55	99.47	0.91	0.89	13	conclusive
GCA_018649665.1	s__UBA1328 sp018649665	88.308	498	678	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905614375.1	s__UBA1328 sp905614375	84.3421	292	678	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018650845.1	s__UBA1328 sp018650845	79.6236	347	678	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	99.74	99.74	0.93	0.93	2	-
GCA_013204545.1	s__UBA1328 sp013204545	78.1798	226	678	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002501045.1	s__UBA1328 sp002501045	77.6358	201	678	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	99.73	99.73	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-03-16 09:24:09,672] [INFO] GTDB search result was written to OceanDNA-b14596/result_gtdb.tsv
[2023-03-16 09:24:09,674] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:24:09,676] [INFO] DFAST_QC result json was written to OceanDNA-b14596/dqc_result.json
[2023-03-16 09:24:09,676] [INFO] DFAST_QC completed!
[2023-03-16 09:24:09,676] [INFO] Total running time: 0h1m0s