[2023-03-19 02:05:11,578] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:05:11,578] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:05:11,578] [INFO] DQC Reference Directory: /var/lib/cwl/stg7da1654a-2ff8-46f7-ae3f-0d12e60cbe1f/dqc_reference
[2023-03-19 02:05:13,263] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:05:13,264] [INFO] Task started: Prodigal
[2023-03-19 02:05:13,264] [INFO] Running command: cat /var/lib/cwl/stgc799c544-66ba-45d6-800a-6aef2cd6afba/OceanDNA-b19917.fa | prodigal -d OceanDNA-b19917/cds.fna -a OceanDNA-b19917/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:05:16,465] [INFO] Task succeeded: Prodigal
[2023-03-19 02:05:16,465] [INFO] Task started: HMMsearch
[2023-03-19 02:05:16,465] [INFO] Running command: hmmsearch --tblout OceanDNA-b19917/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7da1654a-2ff8-46f7-ae3f-0d12e60cbe1f/dqc_reference/reference_markers.hmm OceanDNA-b19917/protein.faa > /dev/null
[2023-03-19 02:05:16,602] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:05:16,603] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc799c544-66ba-45d6-800a-6aef2cd6afba/OceanDNA-b19917.fa]
[2023-03-19 02:05:16,611] [INFO] Query marker FASTA was written to OceanDNA-b19917/markers.fasta
[2023-03-19 02:05:16,611] [INFO] Task started: Blastn
[2023-03-19 02:05:16,611] [INFO] Running command: blastn -query OceanDNA-b19917/markers.fasta -db /var/lib/cwl/stg7da1654a-2ff8-46f7-ae3f-0d12e60cbe1f/dqc_reference/reference_markers.fasta -out OceanDNA-b19917/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:05:18,063] [INFO] Task succeeded: Blastn
[2023-03-19 02:05:18,064] [INFO] Selected 3 target genomes.
[2023-03-19 02:05:18,064] [INFO] Target genome list was writen to OceanDNA-b19917/target_genomes.txt
[2023-03-19 02:05:18,066] [INFO] Task started: fastANI
[2023-03-19 02:05:18,066] [INFO] Running command: fastANI --query /var/lib/cwl/stgc799c544-66ba-45d6-800a-6aef2cd6afba/OceanDNA-b19917.fa --refList OceanDNA-b19917/target_genomes.txt --output OceanDNA-b19917/fastani_result.tsv --threads 1
[2023-03-19 02:05:19,491] [INFO] Task succeeded: fastANI
[2023-03-19 02:05:19,491] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7da1654a-2ff8-46f7-ae3f-0d12e60cbe1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:05:19,491] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7da1654a-2ff8-46f7-ae3f-0d12e60cbe1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:05:19,492] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:05:19,492] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 02:05:19,492] [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
--------------------------------------------------------------------------------
[2023-03-19 02:05:19,492] [INFO] DFAST Taxonomy check result was written to OceanDNA-b19917/tc_result.tsv
[2023-03-19 02:05:19,492] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:05:19,492] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:05:19,492] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7da1654a-2ff8-46f7-ae3f-0d12e60cbe1f/dqc_reference/checkm_data
[2023-03-19 02:05:19,495] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:05:19,497] [INFO] Task started: CheckM
[2023-03-19 02:05:19,497] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b19917/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b19917/checkm_input OceanDNA-b19917/checkm_result
[2023-03-19 02:05:34,660] [INFO] Task succeeded: CheckM
[2023-03-19 02:05:34,660] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.54%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 02:05:34,662] [INFO] ===== Completeness check finished =====
[2023-03-19 02:05:34,662] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:05:34,662] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b19917/markers.fasta)
[2023-03-19 02:05:34,662] [INFO] Task started: Blastn
[2023-03-19 02:05:34,662] [INFO] Running command: blastn -query OceanDNA-b19917/markers.fasta -db /var/lib/cwl/stg7da1654a-2ff8-46f7-ae3f-0d12e60cbe1f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b19917/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:05:35,312] [INFO] Task succeeded: Blastn
[2023-03-19 02:05:35,313] [INFO] Selected 11 target genomes.
[2023-03-19 02:05:35,313] [INFO] Target genome list was writen to OceanDNA-b19917/target_genomes_gtdb.txt
[2023-03-19 02:05:35,570] [INFO] Task started: fastANI
[2023-03-19 02:05:35,570] [INFO] Running command: fastANI --query /var/lib/cwl/stgc799c544-66ba-45d6-800a-6aef2cd6afba/OceanDNA-b19917.fa --refList OceanDNA-b19917/target_genomes_gtdb.txt --output OceanDNA-b19917/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:05:39,230] [INFO] Task succeeded: fastANI
[2023-03-19 02:05:39,234] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:05:39,234] [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_018692355.1	s__GCA-2722105 sp018692355	92.1127	104	129	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-2722105	95.0	99.23	99.02	0.79	0.73	14	-
GCA_015658495.1	s__GCA-2722105 sp015658495	81.001	69	129	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-2722105	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018674095.1	s__GCA-2722105 sp018674095	78.7752	54	129	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__UBA1611;g__GCA-2722105	95.0	99.41	99.30	0.88	0.82	13	-
--------------------------------------------------------------------------------
[2023-03-19 02:05:39,234] [INFO] GTDB search result was written to OceanDNA-b19917/result_gtdb.tsv
[2023-03-19 02:05:39,234] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:05:39,235] [INFO] DFAST_QC result json was written to OceanDNA-b19917/dqc_result.json
[2023-03-19 02:05:39,235] [INFO] DFAST_QC completed!
[2023-03-19 02:05:39,235] [INFO] Total running time: 0h0m28s