[2023-03-16 08:59:43,909] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:59:43,909] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:59:43,909] [INFO] DQC Reference Directory: /var/lib/cwl/stgab30d4f5-674f-4b66-8922-f7e0c83f9044/dqc_reference
[2023-03-16 08:59:45,387] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:59:45,387] [INFO] Task started: Prodigal
[2023-03-16 08:59:45,387] [INFO] Running command: cat /var/lib/cwl/stg4bb5ecef-bef5-4368-81e0-9d9acaa2fa1e/OceanDNA-b18085.fa | prodigal -d OceanDNA-b18085/cds.fna -a OceanDNA-b18085/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:59:49,049] [INFO] Task succeeded: Prodigal
[2023-03-16 08:59:49,049] [INFO] Task started: HMMsearch
[2023-03-16 08:59:49,049] [INFO] Running command: hmmsearch --tblout OceanDNA-b18085/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab30d4f5-674f-4b66-8922-f7e0c83f9044/dqc_reference/reference_markers.hmm OceanDNA-b18085/protein.faa > /dev/null
[2023-03-16 08:59:49,243] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:59:49,244] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4bb5ecef-bef5-4368-81e0-9d9acaa2fa1e/OceanDNA-b18085.fa]
[2023-03-16 08:59:49,250] [INFO] Query marker FASTA was written to OceanDNA-b18085/markers.fasta
[2023-03-16 08:59:49,252] [INFO] Task started: Blastn
[2023-03-16 08:59:49,252] [INFO] Running command: blastn -query OceanDNA-b18085/markers.fasta -db /var/lib/cwl/stgab30d4f5-674f-4b66-8922-f7e0c83f9044/dqc_reference/reference_markers.fasta -out OceanDNA-b18085/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:59:51,858] [INFO] Task succeeded: Blastn
[2023-03-16 08:59:51,858] [INFO] Selected 12 target genomes.
[2023-03-16 08:59:51,859] [INFO] Target genome list was writen to OceanDNA-b18085/target_genomes.txt
[2023-03-16 08:59:51,867] [INFO] Task started: fastANI
[2023-03-16 08:59:51,867] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bb5ecef-bef5-4368-81e0-9d9acaa2fa1e/OceanDNA-b18085.fa --refList OceanDNA-b18085/target_genomes.txt --output OceanDNA-b18085/fastani_result.tsv --threads 1
[2023-03-16 08:59:57,966] [INFO] Task succeeded: fastANI
[2023-03-16 08:59:57,967] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab30d4f5-674f-4b66-8922-f7e0c83f9044/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:59:57,967] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab30d4f5-674f-4b66-8922-f7e0c83f9044/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:59:57,967] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:59:57,967] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 08:59:57,967] [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 08:59:57,968] [INFO] DFAST Taxonomy check result was written to OceanDNA-b18085/tc_result.tsv
[2023-03-16 08:59:57,968] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:59:57,968] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:59:57,968] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab30d4f5-674f-4b66-8922-f7e0c83f9044/dqc_reference/checkm_data
[2023-03-16 08:59:57,971] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:59:58,034] [INFO] Task started: CheckM
[2023-03-16 08:59:58,034] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b18085/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b18085/checkm_input OceanDNA-b18085/checkm_result
[2023-03-16 09:00:14,269] [INFO] Task succeeded: CheckM
[2023-03-16 09:00:14,270] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:00:14,271] [INFO] ===== Completeness check finished =====
[2023-03-16 09:00:14,271] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:00:14,271] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b18085/markers.fasta)
[2023-03-16 09:00:14,273] [INFO] Task started: Blastn
[2023-03-16 09:00:14,273] [INFO] Running command: blastn -query OceanDNA-b18085/markers.fasta -db /var/lib/cwl/stgab30d4f5-674f-4b66-8922-f7e0c83f9044/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b18085/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:00:15,081] [INFO] Task succeeded: Blastn
[2023-03-16 09:00:15,082] [INFO] Selected 11 target genomes.
[2023-03-16 09:00:15,082] [INFO] Target genome list was writen to OceanDNA-b18085/target_genomes_gtdb.txt
[2023-03-16 09:00:15,092] [INFO] Task started: fastANI
[2023-03-16 09:00:15,093] [INFO] Running command: fastANI --query /var/lib/cwl/stg4bb5ecef-bef5-4368-81e0-9d9acaa2fa1e/OceanDNA-b18085.fa --refList OceanDNA-b18085/target_genomes_gtdb.txt --output OceanDNA-b18085/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:00:17,889] [INFO] Task succeeded: fastANI
[2023-03-16 09:00:17,894] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 09:00:17,894] [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_000402815.1	s__Marinisoma atlanticum	92.6834	213	238	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	99.54	99.22	0.95	0.89	4	-
GCA_002701645.1	s__Marinisoma sp002701645	84.234	151	238	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014240005.1	s__Marinisoma sp014240005	83.8665	173	238	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	96.63	96.63	0.87	0.87	2	-
GCA_905182795.1	s__Marinisoma sp905182795	83.5917	208	238	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000402755.1	s__Marinisoma sp000402755	83.5044	177	238	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	95.42	95.16	0.79	0.76	17	-
GCA_902624275.1	s__Marinisoma sp902624275	77.8437	69	238	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 09:00:17,894] [INFO] GTDB search result was written to OceanDNA-b18085/result_gtdb.tsv
[2023-03-16 09:00:17,895] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:00:17,895] [INFO] DFAST_QC result json was written to OceanDNA-b18085/dqc_result.json
[2023-03-16 09:00:17,895] [INFO] DFAST_QC completed!
[2023-03-16 09:00:17,895] [INFO] Total running time: 0h0m34s