[2023-03-15 03:56:21,753] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:56:21,753] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:56:21,753] [INFO] DQC Reference Directory: /var/lib/cwl/stgb7fc8f1e-a59f-462c-90a4-920a18ee1ecb/dqc_reference
[2023-03-15 03:56:23,405] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:56:23,405] [INFO] Task started: Prodigal
[2023-03-15 03:56:23,405] [INFO] Running command: cat /var/lib/cwl/stg3f1b3c8f-028a-4b64-9849-3e423a8008b1/OceanDNA-b18119.fa | prodigal -d OceanDNA-b18119/cds.fna -a OceanDNA-b18119/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:56:26,512] [INFO] Task succeeded: Prodigal
[2023-03-15 03:56:26,512] [INFO] Task started: HMMsearch
[2023-03-15 03:56:26,513] [INFO] Running command: hmmsearch --tblout OceanDNA-b18119/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb7fc8f1e-a59f-462c-90a4-920a18ee1ecb/dqc_reference/reference_markers.hmm OceanDNA-b18119/protein.faa > /dev/null
[2023-03-15 03:56:26,720] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:56:26,721] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3f1b3c8f-028a-4b64-9849-3e423a8008b1/OceanDNA-b18119.fa]
[2023-03-15 03:56:26,726] [INFO] Query marker FASTA was written to OceanDNA-b18119/markers.fasta
[2023-03-15 03:56:26,728] [INFO] Task started: Blastn
[2023-03-15 03:56:26,728] [INFO] Running command: blastn -query OceanDNA-b18119/markers.fasta -db /var/lib/cwl/stgb7fc8f1e-a59f-462c-90a4-920a18ee1ecb/dqc_reference/reference_markers.fasta -out OceanDNA-b18119/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:56:29,095] [INFO] Task succeeded: Blastn
[2023-03-15 03:56:29,096] [INFO] Selected 17 target genomes.
[2023-03-15 03:56:29,096] [INFO] Target genome list was writen to OceanDNA-b18119/target_genomes.txt
[2023-03-15 03:56:29,113] [INFO] Task started: fastANI
[2023-03-15 03:56:29,113] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f1b3c8f-028a-4b64-9849-3e423a8008b1/OceanDNA-b18119.fa --refList OceanDNA-b18119/target_genomes.txt --output OceanDNA-b18119/fastani_result.tsv --threads 1
[2023-03-15 03:56:37,818] [INFO] Task succeeded: fastANI
[2023-03-15 03:56:37,818] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb7fc8f1e-a59f-462c-90a4-920a18ee1ecb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:56:37,819] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb7fc8f1e-a59f-462c-90a4-920a18ee1ecb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:56:37,819] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:56:37,819] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 03:56:37,819] [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 03:56:37,819] [INFO] DFAST Taxonomy check result was written to OceanDNA-b18119/tc_result.tsv
[2023-03-15 03:56:37,819] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:56:37,819] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:56:37,819] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb7fc8f1e-a59f-462c-90a4-920a18ee1ecb/dqc_reference/checkm_data
[2023-03-15 03:56:37,822] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:56:37,824] [INFO] Task started: CheckM
[2023-03-15 03:56:37,824] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b18119/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b18119/checkm_input OceanDNA-b18119/checkm_result
[2023-03-15 03:56:52,488] [INFO] Task succeeded: CheckM
[2023-03-15 03:56:52,488] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.18%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:56:52,490] [INFO] ===== Completeness check finished =====
[2023-03-15 03:56:52,490] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:56:52,490] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b18119/markers.fasta)
[2023-03-15 03:56:52,490] [INFO] Task started: Blastn
[2023-03-15 03:56:52,490] [INFO] Running command: blastn -query OceanDNA-b18119/markers.fasta -db /var/lib/cwl/stgb7fc8f1e-a59f-462c-90a4-920a18ee1ecb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b18119/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:56:53,192] [INFO] Task succeeded: Blastn
[2023-03-15 03:56:53,193] [INFO] Selected 11 target genomes.
[2023-03-15 03:56:53,193] [INFO] Target genome list was writen to OceanDNA-b18119/target_genomes_gtdb.txt
[2023-03-15 03:56:53,210] [INFO] Task started: fastANI
[2023-03-15 03:56:53,210] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f1b3c8f-028a-4b64-9849-3e423a8008b1/OceanDNA-b18119.fa --refList OceanDNA-b18119/target_genomes_gtdb.txt --output OceanDNA-b18119/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:56:54,975] [INFO] Task succeeded: fastANI
[2023-03-15 03:56:54,981] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 03:56:54,982] [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_902578385.1	s__Marinisoma sp002710515	79.5323	121	194	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	97.88	96.56	0.86	0.83	7	-
GCA_016777965.1	s__Marinisoma sp016777965	79.2476	55	194	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902599655.1	s__Marinisoma sp902599655	79.1076	90	194	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	97.53	97.28	0.66	0.66	3	-
GCA_902576865.1	s__Marinisoma sp902576865	79.0875	100	194	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	96.64	96.64	0.80	0.80	2	-
GCA_902525615.1	s__Marinisoma sp902525615	79.0406	105	194	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902538565.1	s__Marinisoma sp902538565	79.0099	126	194	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	99.07	99.04	0.96	0.96	3	-
GCA_902526795.1	s__Marinisoma sp902526795	78.7755	112	194	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000402655.1	s__Marinisoma sp000402655	78.7352	136	194	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	96.42	95.83	0.93	0.92	4	-
GCA_902624275.1	s__Marinisoma sp902624275	78.5021	114	194	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902624575.1	s__Marinisoma sp902624575	78.1574	54	194	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 03:56:54,982] [INFO] GTDB search result was written to OceanDNA-b18119/result_gtdb.tsv
[2023-03-15 03:56:54,982] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:56:54,983] [INFO] DFAST_QC result json was written to OceanDNA-b18119/dqc_result.json
[2023-03-15 03:56:54,983] [INFO] DFAST_QC completed!
[2023-03-15 03:56:54,983] [INFO] Total running time: 0h0m33s