[2023-03-15 20:49:38,877] [INFO] DFAST_QC pipeline started.
[2023-03-15 20:49:38,878] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 20:49:38,878] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2e3d5a9-786d-410e-987e-1426797ee2af/dqc_reference
[2023-03-15 20:49:40,015] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 20:49:40,015] [INFO] Task started: Prodigal
[2023-03-15 20:49:40,015] [INFO] Running command: cat /var/lib/cwl/stgabc561b3-10d1-4b99-b0e0-2c0efebbab6a/OceanDNA-b14425.fa | prodigal -d OceanDNA-b14425/cds.fna -a OceanDNA-b14425/protein.faa -g 11 -q > /dev/null
[2023-03-15 20:49:50,709] [INFO] Task succeeded: Prodigal
[2023-03-15 20:49:50,710] [INFO] Task started: HMMsearch
[2023-03-15 20:49:50,710] [INFO] Running command: hmmsearch --tblout OceanDNA-b14425/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2e3d5a9-786d-410e-987e-1426797ee2af/dqc_reference/reference_markers.hmm OceanDNA-b14425/protein.faa > /dev/null
[2023-03-15 20:49:50,854] [INFO] Task succeeded: HMMsearch
[2023-03-15 20:49:50,855] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgabc561b3-10d1-4b99-b0e0-2c0efebbab6a/OceanDNA-b14425.fa]
[2023-03-15 20:49:50,869] [INFO] Query marker FASTA was written to OceanDNA-b14425/markers.fasta
[2023-03-15 20:49:50,869] [INFO] Task started: Blastn
[2023-03-15 20:49:50,869] [INFO] Running command: blastn -query OceanDNA-b14425/markers.fasta -db /var/lib/cwl/stgc2e3d5a9-786d-410e-987e-1426797ee2af/dqc_reference/reference_markers.fasta -out OceanDNA-b14425/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:49:51,369] [INFO] Task succeeded: Blastn
[2023-03-15 20:49:51,370] [INFO] Selected 11 target genomes.
[2023-03-15 20:49:51,370] [INFO] Target genome list was writen to OceanDNA-b14425/target_genomes.txt
[2023-03-15 20:49:51,376] [INFO] Task started: fastANI
[2023-03-15 20:49:51,376] [INFO] Running command: fastANI --query /var/lib/cwl/stgabc561b3-10d1-4b99-b0e0-2c0efebbab6a/OceanDNA-b14425.fa --refList OceanDNA-b14425/target_genomes.txt --output OceanDNA-b14425/fastani_result.tsv --threads 1
[2023-03-15 20:49:56,984] [INFO] Task succeeded: fastANI
[2023-03-15 20:49:56,985] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2e3d5a9-786d-410e-987e-1426797ee2af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 20:49:56,985] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2e3d5a9-786d-410e-987e-1426797ee2af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 20:49:56,985] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 20:49:56,985] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 20:49:56,985] [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 20:49:56,985] [INFO] DFAST Taxonomy check result was written to OceanDNA-b14425/tc_result.tsv
[2023-03-15 20:49:56,986] [INFO] ===== Taxonomy check completed =====
[2023-03-15 20:49:56,986] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 20:49:56,986] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2e3d5a9-786d-410e-987e-1426797ee2af/dqc_reference/checkm_data
[2023-03-15 20:49:56,988] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 20:49:56,992] [INFO] Task started: CheckM
[2023-03-15 20:49:56,992] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b14425/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b14425/checkm_input OceanDNA-b14425/checkm_result
[2023-03-15 20:50:27,949] [INFO] Task succeeded: CheckM
[2023-03-15 20:50:27,950] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.58%
Contamintation: 4.63%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 20:50:27,952] [INFO] ===== Completeness check finished =====
[2023-03-15 20:50:27,952] [INFO] ===== Start GTDB Search =====
[2023-03-15 20:50:27,952] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b14425/markers.fasta)
[2023-03-15 20:50:27,953] [INFO] Task started: Blastn
[2023-03-15 20:50:27,953] [INFO] Running command: blastn -query OceanDNA-b14425/markers.fasta -db /var/lib/cwl/stgc2e3d5a9-786d-410e-987e-1426797ee2af/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b14425/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:50:28,667] [INFO] Task succeeded: Blastn
[2023-03-15 20:50:28,667] [INFO] Selected 14 target genomes.
[2023-03-15 20:50:28,667] [INFO] Target genome list was writen to OceanDNA-b14425/target_genomes_gtdb.txt
[2023-03-15 20:50:28,927] [INFO] Task started: fastANI
[2023-03-15 20:50:28,927] [INFO] Running command: fastANI --query /var/lib/cwl/stgabc561b3-10d1-4b99-b0e0-2c0efebbab6a/OceanDNA-b14425.fa --refList OceanDNA-b14425/target_genomes_gtdb.txt --output OceanDNA-b14425/fastani_result_gtdb.tsv --threads 1
[2023-03-15 20:50:35,315] [INFO] Task succeeded: fastANI
[2023-03-15 20:50:35,320] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 20:50:35,320] [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_012959765.1	s__UBA1328 sp012959765	78.652	292	615	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	99.88	99.88	0.97	0.97	2	-
GCA_018650845.1	s__UBA1328 sp018650845	77.5861	223	615	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	99.74	99.74	0.93	0.93	2	-
GCA_002501045.1	s__UBA1328 sp002501045	77.288	169	615	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	99.73	99.73	0.84	0.84	2	-
GCA_018649665.1	s__UBA1328 sp018649665	77.2752	197	615	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018673955.1	s__UBA1328 sp018673955	77.2409	157	615	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	99.55	99.47	0.91	0.89	13	-
GCA_002306815.1	s__UBA1328 sp002306815	76.4679	96	615	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	98.45	96.89	0.85	0.79	5	-
GCA_002313245.1	s__UBA9455 sp002313245	76.3332	113	615	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA9455	95.0	97.93	97.22	0.78	0.67	5	-
--------------------------------------------------------------------------------
[2023-03-15 20:50:35,320] [INFO] GTDB search result was written to OceanDNA-b14425/result_gtdb.tsv
[2023-03-15 20:50:35,320] [INFO] ===== GTDB Search completed =====
[2023-03-15 20:50:35,321] [INFO] DFAST_QC result json was written to OceanDNA-b14425/dqc_result.json
[2023-03-15 20:50:35,321] [INFO] DFAST_QC completed!
[2023-03-15 20:50:35,321] [INFO] Total running time: 0h0m56s