[2023-03-17 07:44:36,992] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:44:36,992] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:44:36,992] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe122880-ab7b-4055-a9b0-b44491b3c83e/dqc_reference
[2023-03-17 07:44:38,850] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:44:38,850] [INFO] Task started: Prodigal
[2023-03-17 07:44:38,851] [INFO] Running command: cat /var/lib/cwl/stg5af4a660-ab0d-4284-996a-38581afe4338/OceanDNA-b21009.fa | prodigal -d OceanDNA-b21009/cds.fna -a OceanDNA-b21009/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:45:05,486] [INFO] Task succeeded: Prodigal
[2023-03-17 07:45:05,486] [INFO] Task started: HMMsearch
[2023-03-17 07:45:05,486] [INFO] Running command: hmmsearch --tblout OceanDNA-b21009/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe122880-ab7b-4055-a9b0-b44491b3c83e/dqc_reference/reference_markers.hmm OceanDNA-b21009/protein.faa > /dev/null
[2023-03-17 07:45:05,692] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:45:05,693] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5af4a660-ab0d-4284-996a-38581afe4338/OceanDNA-b21009.fa]
[2023-03-17 07:45:05,721] [INFO] Query marker FASTA was written to OceanDNA-b21009/markers.fasta
[2023-03-17 07:45:05,721] [INFO] Task started: Blastn
[2023-03-17 07:45:05,721] [INFO] Running command: blastn -query OceanDNA-b21009/markers.fasta -db /var/lib/cwl/stgbe122880-ab7b-4055-a9b0-b44491b3c83e/dqc_reference/reference_markers.fasta -out OceanDNA-b21009/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:45:06,341] [INFO] Task succeeded: Blastn
[2023-03-17 07:45:06,342] [INFO] Selected 21 target genomes.
[2023-03-17 07:45:06,343] [INFO] Target genome list was writen to OceanDNA-b21009/target_genomes.txt
[2023-03-17 07:45:06,351] [INFO] Task started: fastANI
[2023-03-17 07:45:06,351] [INFO] Running command: fastANI --query /var/lib/cwl/stg5af4a660-ab0d-4284-996a-38581afe4338/OceanDNA-b21009.fa --refList OceanDNA-b21009/target_genomes.txt --output OceanDNA-b21009/fastani_result.tsv --threads 1
[2023-03-17 07:45:23,906] [INFO] Task succeeded: fastANI
[2023-03-17 07:45:23,906] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe122880-ab7b-4055-a9b0-b44491b3c83e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:45:23,906] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe122880-ab7b-4055-a9b0-b44491b3c83e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:45:23,907] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:45:23,907] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 07:45:23,907] [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
--------------------------------------------------------------------------------
[2023-03-17 07:45:23,907] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21009/tc_result.tsv
[2023-03-17 07:45:23,907] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:45:23,907] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:45:23,907] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe122880-ab7b-4055-a9b0-b44491b3c83e/dqc_reference/checkm_data
[2023-03-17 07:45:23,910] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:45:23,915] [INFO] Task started: CheckM
[2023-03-17 07:45:23,916] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21009/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21009/checkm_input OceanDNA-b21009/checkm_result
[2023-03-17 07:46:28,729] [INFO] Task succeeded: CheckM
[2023-03-17 07:46:28,730] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:46:28,733] [INFO] ===== Completeness check finished =====
[2023-03-17 07:46:28,733] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:46:28,733] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21009/markers.fasta)
[2023-03-17 07:46:28,733] [INFO] Task started: Blastn
[2023-03-17 07:46:28,734] [INFO] Running command: blastn -query OceanDNA-b21009/markers.fasta -db /var/lib/cwl/stgbe122880-ab7b-4055-a9b0-b44491b3c83e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21009/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:46:29,877] [INFO] Task succeeded: Blastn
[2023-03-17 07:46:29,878] [INFO] Selected 22 target genomes.
[2023-03-17 07:46:29,878] [INFO] Target genome list was writen to OceanDNA-b21009/target_genomes_gtdb.txt
[2023-03-17 07:46:29,897] [INFO] Task started: fastANI
[2023-03-17 07:46:29,897] [INFO] Running command: fastANI --query /var/lib/cwl/stg5af4a660-ab0d-4284-996a-38581afe4338/OceanDNA-b21009.fa --refList OceanDNA-b21009/target_genomes_gtdb.txt --output OceanDNA-b21009/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:46:44,930] [INFO] Task succeeded: fastANI
[2023-03-17 07:46:44,936] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 07:46:44,936] [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_012960035.1	s__DUBZ01 sp012960035	94.3031	1216	1386	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__DUBZ01	95.0	99.83	99.83	0.93	0.93	2	-
GCA_012959805.1	s__UBA4427 sp012959805	79.2683	66	1386	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__UBA4427	95.0	99.86	99.86	0.88	0.88	2	-
GCA_002709835.1	s__UBA4427 sp002709835	76.2052	56	1386	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__UBA4427	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002390675.1	s__UBA4427 sp002390675	76.2006	62	1386	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__UBA4427	95.0	99.70	99.70	0.94	0.94	2	-
GCA_016713665.1	s__JADJOR01 sp016713665	75.5028	75	1386	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__JADJOR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002719955.1	s__UBA4427 sp002719955	75.3899	50	1386	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__UBA4427	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215605.1	s__JABSQW01 sp013215605	75.326	69	1386	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__JABSQW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793725.1	s__JAEUJP01 sp016793725	74.5966	51	1386	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__JAEUJP01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 07:46:44,936] [INFO] GTDB search result was written to OceanDNA-b21009/result_gtdb.tsv
[2023-03-17 07:46:44,936] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:46:44,937] [INFO] DFAST_QC result json was written to OceanDNA-b21009/dqc_result.json
[2023-03-17 07:46:44,937] [INFO] DFAST_QC completed!
[2023-03-17 07:46:44,937] [INFO] Total running time: 0h2m8s