[2023-03-15 22:44:22,145] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:44:22,163] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:44:22,163] [INFO] DQC Reference Directory: /var/lib/cwl/stgca9aed88-5d49-4fd8-96f4-1fb010751d1e/dqc_reference
[2023-03-15 22:44:23,286] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:44:23,287] [INFO] Task started: Prodigal
[2023-03-15 22:44:23,287] [INFO] Running command: cat /var/lib/cwl/stg6d72d07e-68f5-42d8-b72b-4bf2ecd1b36f/OceanDNA-b2150.fa | prodigal -d OceanDNA-b2150/cds.fna -a OceanDNA-b2150/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:44:25,871] [INFO] Task succeeded: Prodigal
[2023-03-15 22:44:25,871] [INFO] Task started: HMMsearch
[2023-03-15 22:44:25,871] [INFO] Running command: hmmsearch --tblout OceanDNA-b2150/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca9aed88-5d49-4fd8-96f4-1fb010751d1e/dqc_reference/reference_markers.hmm OceanDNA-b2150/protein.faa > /dev/null
[2023-03-15 22:44:26,020] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:44:26,021] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg6d72d07e-68f5-42d8-b72b-4bf2ecd1b36f/OceanDNA-b2150.fa]
[2023-03-15 22:44:26,153] [INFO] Query marker FASTA was written to OceanDNA-b2150/markers.fasta
[2023-03-15 22:44:26,155] [INFO] Task started: Blastn
[2023-03-15 22:44:26,155] [INFO] Running command: blastn -query OceanDNA-b2150/markers.fasta -db /var/lib/cwl/stgca9aed88-5d49-4fd8-96f4-1fb010751d1e/dqc_reference/reference_markers.fasta -out OceanDNA-b2150/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:44:26,866] [INFO] Task succeeded: Blastn
[2023-03-15 22:44:26,919] [INFO] Selected 15 target genomes.
[2023-03-15 22:44:26,920] [INFO] Target genome list was writen to OceanDNA-b2150/target_genomes.txt
[2023-03-15 22:44:26,929] [INFO] Task started: fastANI
[2023-03-15 22:44:26,929] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d72d07e-68f5-42d8-b72b-4bf2ecd1b36f/OceanDNA-b2150.fa --refList OceanDNA-b2150/target_genomes.txt --output OceanDNA-b2150/fastani_result.tsv --threads 1
[2023-03-15 22:44:32,278] [INFO] Task succeeded: fastANI
[2023-03-15 22:44:32,278] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca9aed88-5d49-4fd8-96f4-1fb010751d1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:44:32,279] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca9aed88-5d49-4fd8-96f4-1fb010751d1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:44:32,279] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:44:32,279] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 22:44:32,279] [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 22:44:32,282] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2150/tc_result.tsv
[2023-03-15 22:44:32,290] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:44:32,290] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:44:32,290] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca9aed88-5d49-4fd8-96f4-1fb010751d1e/dqc_reference/checkm_data
[2023-03-15 22:44:32,341] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:44:32,822] [INFO] Task started: CheckM
[2023-03-15 22:44:32,822] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2150/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2150/checkm_input OceanDNA-b2150/checkm_result
[2023-03-15 22:44:50,657] [INFO] Task succeeded: CheckM
[2023-03-15 22:44:50,658] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 22:44:50,820] [INFO] ===== Completeness check finished =====
[2023-03-15 22:44:50,820] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:44:50,820] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2150/markers.fasta)
[2023-03-15 22:44:50,822] [INFO] Task started: Blastn
[2023-03-15 22:44:50,822] [INFO] Running command: blastn -query OceanDNA-b2150/markers.fasta -db /var/lib/cwl/stgca9aed88-5d49-4fd8-96f4-1fb010751d1e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2150/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:44:51,885] [INFO] Task succeeded: Blastn
[2023-03-15 22:44:51,891] [INFO] Selected 14 target genomes.
[2023-03-15 22:44:51,891] [INFO] Target genome list was writen to OceanDNA-b2150/target_genomes_gtdb.txt
[2023-03-15 22:44:52,071] [INFO] Task started: fastANI
[2023-03-15 22:44:52,071] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d72d07e-68f5-42d8-b72b-4bf2ecd1b36f/OceanDNA-b2150.fa --refList OceanDNA-b2150/target_genomes_gtdb.txt --output OceanDNA-b2150/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:44:54,821] [INFO] Task succeeded: fastANI
[2023-03-15 22:44:54,828] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 22:44:54,829] [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_902521955.1	s__Actinomarina sp902521955	93.177	134	169	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902519215.1	s__Actinomarina sp902519215	91.4214	138	169	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	96.27	96.27	0.84	0.84	2	-
GCA_902555055.1	s__Actinomarina sp902555055	89.3229	127	169	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	79.2356	60	169	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004213405.1	s__Actinomarina sp004213405	79.1216	51	169	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902628045.1	s__Actinomarina sp902628045	78.8903	71	169	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902625455.1	s__Actinomarina sp902625455	78.6755	90	169	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	97.46	97.35	0.85	0.81	4	-
GCA_016777845.1	s__Actinomarina sp016777845	78.6168	60	169	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902596545.1	s__Actinomarina sp902596545	78.5191	86	169	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	98.42	98.42	0.93	0.93	2	-
GCA_003281085.1	s__Actinomarina sp003281085	78.3216	78	169	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	96.17	95.08	0.82	0.73	10	-
GCA_902595195.1	s__Actinomarina sp902595195	77.8955	71	169	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Actinomarinales;f__Actinomarinaceae;g__Actinomarina	95.0	97.26	97.26	0.73	0.73	2	-
--------------------------------------------------------------------------------
[2023-03-15 22:44:54,847] [INFO] GTDB search result was written to OceanDNA-b2150/result_gtdb.tsv
[2023-03-15 22:44:54,889] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:44:54,910] [INFO] DFAST_QC result json was written to OceanDNA-b2150/dqc_result.json
[2023-03-15 22:44:54,910] [INFO] DFAST_QC completed!
[2023-03-15 22:44:54,910] [INFO] Total running time: 0h0m33s